diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..6489772
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,122 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-go@v5
+        with:
+          go-version: '1.24'
+
+      - name: Download dependencies
+        run: go mod download
+
+      - name: Run tests
+        # Note: -race disabled due to pre-existing race conditions in tests that spawn
+        # background goroutines. These should be fixed by adding proper synchronization.
+        run: go test -v ./...
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-go@v5
+        with:
+          go-version: '1.24'
+
+      - name: golangci-lint
+        uses: golangci/golangci-lint-action@v6
+        with:
+          version: latest
+
+  security:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-go@v5
+        with:
+          go-version: '1.24'
+
+      - name: Run gosec
+        uses: securego/gosec@master
+        with:
+          # Exclude G101 (hardcoded credentials - false positive on env var names)
+          # Exclude G115 (integer overflow - false positive for PR numbers)
+          # Exclude G304 (file inclusion - intentional for CLI tools)
+          # Exclude G306 (file permissions - config files don't need 0600)
+          args: -exclude=G101,G115,G304,G306 ./...
+
+  build:
+    runs-on: ubuntu-latest
+    needs: [test, lint]
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-go@v5
+        with:
+          go-version: '1.24'
+
+      - name: Build
+        run: go build -v ./...
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: [build, security]
+    # Only deploy on push to main (not on PRs)
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+
+    permissions:
+      contents: read
+      id-token: write  # Required for Workload Identity Federation
+
+    env:
+      PROJECT_ID: "github-copy-code-examples"
+      SERVICE_NAME: "examples-copier"
+      REGION: "us-central1"
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Authenticate to Google Cloud
+        uses: google-github-actions/auth@v2
+        with:
+          workload_identity_provider: ${{ secrets.GCP_WORKLOAD_IDENTITY_PROVIDER }}
+          service_account: ${{ secrets.GCP_SERVICE_ACCOUNT }}
+
+      - name: Set up Cloud SDK
+        uses: google-github-actions/setup-gcloud@v2
+
+      - name: Deploy to Cloud Run
+        run: |
+          gcloud run deploy $SERVICE_NAME \
+            --source . \
+            --region $REGION \
+            --project $PROJECT_ID \
+            --allow-unauthenticated \
+            --env-vars-file=env-cloudrun.yaml \
+            --max-instances=10 \
+            --cpu=1 \
+            --memory=512Mi \
+            --timeout=300s \
+            --concurrency=80 \
+            --port=8080 \
+            --platform=managed
+
+      - name: Show deployment URL
+        run: |
+          URL=$(gcloud run services describe $SERVICE_NAME \
+            --region $REGION \
+            --project $PROJECT_ID \
+            --format='value(status.url)')
+          echo "🚀 Deployed to: $URL"
+
diff --git a/.gitignore b/.gitignore
index 99d319b..37a0615 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,5 @@
 # Binaries
-examples-copier
+github-copier
 code-copier
 copier
 *.exe
@@ -23,19 +23,21 @@ go.work
 # Environment files with secrets (working files - create from templates in configs/)
 # Working files (create from templates):
 #   env.yaml - App Engine deployment config (from configs/env.yaml.*)
-#   env-cloudrun.yaml - Cloud Run deployment config (from configs/env.yaml.*)
 #   .env - Local development config (from configs/.env.local.example)
+#   .env.test - Test config (from testdata/.env.test)
+# Note: env-cloudrun.yaml is committed (contains no secrets, only Secret Manager references)
 env.yaml
-env-cloudrun.yaml
 .env
 .env.local
+.env.test
 .env.production
 .env.*.local
 
-# Explicitly keep template files in configs/ directory (these should be tracked)
+# Explicitly keep template files (these should be tracked)
 !configs/env.yaml.example
 !configs/env.yaml.production
 !configs/.env.local.example
+!testdata/.env.test
 
 # Private keys
 *.pem
@@ -58,3 +60,4 @@ Thumbs.db
 # Temporary files
 tmp/
 temp/
+RECOMMENDATIONS.md
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..d8c909a
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,36 @@
+repos:
+  # Secrets detection
+  - repo: https://github.com/gitleaks/gitleaks
+    rev: v8.21.2
+    hooks:
+      - id: gitleaks
+
+  # Go linting
+  - repo: https://github.com/golangci/golangci-lint
+    rev: v1.62.2
+    hooks:
+      - id: golangci-lint
+
+  # Local Go hooks
+  - repo: local
+    hooks:
+      - id: go-fmt
+        name: go fmt
+        entry: gofmt -w
+        language: system
+        types: [go]
+
+      - id: go-vet
+        name: go vet
+        entry: go vet ./...
+        language: system
+        pass_filenames: false
+        types: [go]
+
+      - id: go-build
+        name: go build
+        entry: go build ./...
+        language: system
+        pass_filenames: false
+        types: [go]
+
diff --git a/AGENT.md b/AGENT.md
new file mode 100644
index 0000000..ab2277c
--- /dev/null
+++ b/AGENT.md
@@ -0,0 +1,90 @@
+# Agent Context: GitHub Copier
+
+Webhook service: PR merged → match files → transform paths → copy to target repos.
+
+## File Map
+
+```
+app.go                              # entrypoint, HTTP server
+services/
+  webhook_handler_new.go            # HandleWebhookWithContainer()
+  workflow_processor.go             # ProcessWorkflow() - core logic
+  pattern_matcher.go                # MatchFile(pattern, path) bool
+  github_auth.go                    # ConfigurePermissions() error
+  github_read.go                    # GetFilesChangedInPr(), RetrieveFileContents()
+  github_write_to_target.go         # AddFilesToTargetRepoBranch()
+  github_write_to_source.go         # UpdateDeprecationFile()
+  file_state_service.go             # tracks upload/deprecate queues
+  main_config_loader.go             # LoadConfig() with $ref support
+  service_container.go              # DI container
+types/
+  config.go                         # Workflow, Transformation, SourcePattern structs
+  types.go                          # ChangedFile, UploadKey, UploadFileContent
+configs/environment.go              # Config struct, LoadEnvironment()
+tests/utils.go                      # test helpers, httpmock setup
+```
+
+## Key Types
+
+```go
+// types/config.go
+type PatternType string    // "prefix" | "glob" | "regex"
+type TransformationType string  // "move" | "copy" | "glob" | "regex"
+
+type Workflow struct {
+    Name           string
+    Source         SourceConfig      // Repo, Branch, Patterns []SourcePattern
+    Destination    DestinationConfig // Repo, Branch
+    Transformations []Transformation // Type, From, To, Pattern, Replacement
+    Commit         CommitConfig      // Strategy, Message, PRTitle, AutoMerge
+}
+
+// types/types.go
+type ChangedFile struct { Path, Status string }  // Status: "ADDED"|"MODIFIED"|"DELETED"
+type UploadKey struct { RepoName, BranchPath string }
+```
+
+## Global State (⚠️ mutable)
+
+```go
+// services/github_write_to_target.go
+var FilesToUpload map[UploadKey]UploadFileContent
+// services/github_auth.go
+var InstallationAccessToken string
+var OrgTokens map[string]string
+```
+
+## Config Example
+
+```yaml
+workflows:
+  - name: "sync-docs"
+    source: { repo: "org/src", branch: "main", patterns: [{type: glob, pattern: "docs/**"}] }
+    destination: { repo: "org/dest", branch: "main" }
+    transformations: [{ type: move, from: "docs/", to: "public/" }]
+    commit: { strategy: pr, message: "Sync" }  # strategy: direct|pr
+```
+
+## Test Commands
+
+```bash
+go test ./...                                    # all
+go test ./services/... -run TestWorkflow -v      # specific
+```
+
+## Edit Patterns
+
+| Task | Files to modify |
+|------|-----------------|
+| New transformation | `types/config.go` (TransformationType) → `workflow_processor.go` (processFileForWorkflow) |
+| New pattern type | `types/config.go` (PatternType) → `pattern_matcher.go` |
+| New config field | `types/config.go` (struct) → consumers in `workflow_processor.go` |
+| Webhook logic | `webhook_handler_new.go` |
+
+## Conventions
+
+- Return `error`, never `log.Fatal`
+- Wrap errors: `fmt.Errorf("context: %w", err)`
+- Nil-check GitHub API responses before dereference
+- Tests use `httpmock`; see `tests/utils.go`
+- **Changelog**: Update `CHANGELOG.md` for all notable changes (follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/))
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..96daa5d
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,54 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## 17 Dec 2025
+
+### Added
+- CI/CD pipeline with GitHub Actions (`.github/workflows/ci.yml`)
+  - Test job
+  - Lint job with golangci-lint
+  - Security scanning with gosec
+  - Build verification
+  - Automated deployment to Cloud Run on merge to main (via Workload Identity Federation)
+- Pre-commit hooks for secrets detection and Go linting (`.pre-commit-config.yaml`)
+- AGENT.md for AI agent context
+- Comprehensive test suite for `workflow_processor.go` (843 lines, 94%+ coverage)
+- Integration test harness for local testing (`scripts/integration-test.sh`)
+- Test environment configuration (`testdata/.env.test`)
+
+### Changed
+- Renamed module from `github.com/mongodb/code-example-tooling/code-copier` to `github.com/grove-platform/github-copier`
+- Renamed binary from `examples-copier` to `github-copier`
+- Renamed `test-payloads/` to `testdata/` (Go convention)
+- All `log.Fatal` calls replaced with proper error returns for graceful error handling
+- `FileStateService.filesToDeprecate` changed from single-entry map to slice-based accumulation
+
+### Fixed
+- Deprecation file accumulation bug: multiple deprecated files now correctly accumulate instead of overwriting
+- Nil pointer dereference bugs across GitHub API calls in:
+  - `services/github_read.go`
+  - `services/github_write_to_source.go`
+  - `services/main_config_loader.go`
+  - `services/config_loader.go`
+- DELETED file status handling: GitHub GraphQL API returns uppercase `DELETED` but code checked for lowercase `removed`
+- Graceful shutdown now properly waits for in-flight requests and cleans up resources
+
+### Security
+- Added gitleaks pre-commit hook for secrets detection
+- Added gosec security scanning in CI pipeline
+
+## Initial Release (Migration from mongodb/code-example-tooling)
+
+### Features
+- Webhook service for automated file copying on PR merge
+- Pattern matching support: prefix, glob, regex
+- Transformation types: move, copy, glob, regex
+- Main config system with `$ref` support for distributed workflow configs
+- Commit strategies: direct commit or pull request
+- Health and metrics endpoints
+- Slack notifications for operational visibility
+- MongoDB audit logging (optional)
+- Google Cloud Logging integration
+- Dry-run mode for testing
+
diff --git a/QUICK-REFERENCE.md b/QUICK-REFERENCE.md
index 193ed77..28fe49a 100644
--- a/QUICK-REFERENCE.md
+++ b/QUICK-REFERENCE.md
@@ -6,19 +6,19 @@
 
 ```bash
 # Run with default settings
-./examples-copier
+./github-copier
 
 # Run with custom environment
-./examples-copier -env ./configs/.env.production
+./github-copier -env ./configs/.env.production
 
 # Dry-run mode (no actual commits)
-./examples-copier -dry-run
+./github-copier -dry-run
 
 # Validate configuration only
-./examples-copier -validate
+./github-copier -validate
 
 # Show help
-./examples-copier -help
+./github-copier -help
 ```
 
 ### CLI Validator
@@ -317,10 +317,10 @@ go test ./services -cover
 go build -o test-webhook ./cmd/test-webhook
 
 # Send example payload
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 
 # Dry-run (see payload without sending)
-./test-webhook -payload test-payloads/example-pr-merged.json -dry-run
+./test-webhook -payload testdata/example-pr-merged.json -dry-run
 ```
 
 #### Option 2: Use Real PR Data
@@ -349,7 +349,7 @@ chmod +x scripts/test-with-pr.sh
 ### Test in Dry-Run Mode
 ```bash
 # Start app in dry-run mode
-DRY_RUN=true ./examples-copier &
+DRY_RUN=true ./github-copier &
 
 # Send test webhook
 ./test-webhook -pr 123 -owner myorg -repo myrepo
@@ -360,7 +360,7 @@ DRY_RUN=true ./examples-copier &
 ### Build
 ```bash
 # Main application
-go build -o examples-copier .
+go build -o github-copier .
 
 # CLI validator
 go build -o config-validator ./cmd/config-validator
@@ -369,7 +369,7 @@ go build -o config-validator ./cmd/config-validator
 go build -o test-webhook ./cmd/test-webhook
 
 # All tools
-go build -o examples-copier . && \
+go build -o github-copier . && \
 go build -o config-validator ./cmd/config-validator && \
 go build -o test-webhook ./cmd/test-webhook
 ```
@@ -442,7 +442,7 @@ workflows:
 gcloud app logs tail -s default
 
 # Local logs
-LOG_LEVEL=debug ./examples-copier
+LOG_LEVEL=debug ./github-copier
 ```
 
 ### Validate Config
@@ -460,7 +460,7 @@ LOG_LEVEL=debug ./examples-copier
 
 ### Dry Run
 ```bash
-DRY_RUN=true ./examples-copier
+DRY_RUN=true ./github-copier
 ```
 
 ### Check Health
@@ -499,7 +499,7 @@ gcloud secrets list
 ## File Locations
 
 ```
-examples-copier/
+github-copier/
 ├── README.md                 # Main documentation
 ├── QUICK-REFERENCE.md        # This file
 ├── docs/
@@ -529,8 +529,8 @@ examples-copier/
 - [ ] Set required environment variables
 - [ ] Create `copier-config.yaml` in source repo
 - [ ] Validate config: `./config-validator validate -config copier-config.yaml`
-- [ ] Test in dry-run: `DRY_RUN=true ./examples-copier`
-- [ ] Deploy: `./examples-copier`
+- [ ] Test in dry-run: `DRY_RUN=true ./github-copier`
+- [ ] Deploy: `./github-copier`
 - [ ] Configure GitHub webhook
 - [ ] Monitor: `curl http://localhost:8080/health`
 
diff --git a/README.md b/README.md
index 4d2b29b..db0a9aa 100644
--- a/README.md
+++ b/README.md
@@ -40,13 +40,13 @@ A GitHub app that automatically copies code examples and files from source repos
 ```bash
 # Clone the repository
 git clone https://github.com/your-org/code-example-tooling.git
-cd code-example-tooling/examples-copier
+cd code-example-tooling/github-copier
 
 # Install dependencies
 go mod download
 
 # Build the application
-go build -o examples-copier .
+go build -o github-copier .
 
 # Build CLI tools
 go build -o config-validator ./cmd/config-validator
@@ -137,16 +137,16 @@ workflows:
 
 ```bash
 # Run with default settings
-./examples-copier
+./github-copier
 
 # Run with custom environment file
-./examples-copier -env ./configs/.env.production
+./github-copier -env ./configs/.env.production
 
 # Run in dry-run mode (no actual commits)
-./examples-copier -dry-run
+./github-copier -dry-run
 
 # Validate configuration only
-./examples-copier -validate
+./github-copier -validate
 ```
 
 ## Configuration
@@ -467,7 +467,7 @@ go tool cover -html=coverage.out
 Test without making actual changes:
 
 ```bash
-DRY_RUN=true ./examples-copier
+DRY_RUN=true ./github-copier
 ```
 
 In dry-run mode:
@@ -481,9 +481,9 @@ In dry-run mode:
 Enable detailed logging:
 
 ```bash
-LOG_LEVEL=debug ./examples-copier
+LOG_LEVEL=debug ./github-copier
 # or
-COPIER_DEBUG=true ./examples-copier
+COPIER_DEBUG=true ./github-copier
 ```
 
 ## Architecture
@@ -491,7 +491,7 @@ COPIER_DEBUG=true ./examples-copier
 ### Project Structure
 
 ```
-examples-copier/
+github-copier/
 ├── app.go                    # Main application entry point
 ├── cmd/
 │   ├── config-validator/     # CLI validation tool
@@ -540,15 +540,15 @@ See [DEPLOYMENT.md](./docs/DEPLOYMENT.md) for complete deployment guide.
 ### Google Cloud Run
 
 ```bash
-cd examples-copier
+cd github-copier
 ./scripts/deploy-cloudrun.sh
 ```
 
 ### Docker
 
 ```bash
-docker build -t examples-copier .
-docker run -p 8080:8080 --env-file env.yaml examples-copier
+docker build -t github-copier .
+docker run -p 8080:8080 --env-file env.yaml github-copier
 ```
 
 ## Security
diff --git a/app.go b/app.go
index ac99a28..f104059 100644
--- a/app.go
+++ b/app.go
@@ -11,8 +11,8 @@ import (
 	"syscall"
 	"time"
 
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
-	"github.com/mongodb/code-example-tooling/code-copier/services"
+	"github.com/grove-platform/github-copier/configs"
+	"github.com/grove-platform/github-copier/services"
 )
 
 func main() {
@@ -78,7 +78,10 @@ func main() {
 	defer services.CloseGoogleLogger()
 
 	// Configure GitHub permissions
-	services.ConfigurePermissions()
+	if err := services.ConfigurePermissions(); err != nil {
+		fmt.Printf("❌ Failed to configure GitHub permissions: %v\n", err)
+		os.Exit(1)
+	}
 
 	// Print startup banner
 	printBanner(config, container)
@@ -170,27 +173,50 @@ func startWebServer(config *configs.Config, container *services.ServiceContainer
 		IdleTimeout:  120 * time.Second,
 	}
 
-	// Handle graceful shutdown
+	// Channel to signal server errors
+	serverErr := make(chan error, 1)
+
+	// Start server in goroutine
 	go func() {
-		sigChan := make(chan os.Signal, 1)
-		signal.Notify(sigChan, os.Interrupt, syscall.SIGTERM)
-		<-sigChan
+		services.LogInfo(fmt.Sprintf("Starting web server on port %s", port))
+		if err := server.ListenAndServe(); err != nil && err != http.ErrServerClosed {
+			serverErr <- fmt.Errorf("server error: %w", err)
+		}
+		close(serverErr)
+	}()
 
-		log.Println("Shutting down server...")
-		ctx, cancel := context.WithTimeout(context.Background(), 30*time.Second)
-		defer cancel()
+	// Wait for interrupt signal
+	sigChan := make(chan os.Signal, 1)
+	signal.Notify(sigChan, os.Interrupt, syscall.SIGTERM)
 
-		if err := server.Shutdown(ctx); err != nil {
-			log.Printf("Server shutdown error: %v\n", err)
+	// Block until we receive a signal or server error
+	select {
+	case err := <-serverErr:
+		if err != nil {
+			return err
 		}
-	}()
+	case sig := <-sigChan:
+		log.Printf("Received signal %v, initiating graceful shutdown...", sig)
+	}
+
+	// Graceful shutdown with timeout
+	shutdownCtx, cancel := context.WithTimeout(context.Background(), 30*time.Second)
+	defer cancel()
+
+	log.Println("Waiting for in-flight requests to complete...")
+	if err := server.Shutdown(shutdownCtx); err != nil {
+		log.Printf("Server shutdown error: %v", err)
+	} else {
+		log.Println("Server stopped accepting new connections")
+	}
 
-	// Start server
-	services.LogInfo(fmt.Sprintf("Starting web server on port %s", port))
-	if err := server.ListenAndServe(); err != nil && err != http.ErrServerClosed {
-		return fmt.Errorf("server error: %w", err)
+	// Cleanup resources (flush audit logs, close connections)
+	log.Println("Cleaning up resources...")
+	if err := container.Close(shutdownCtx); err != nil {
+		log.Printf("Cleanup error: %v", err)
 	}
 
+	log.Println("Shutdown complete")
 	return nil
 }
 
diff --git a/cmd/config-validator/README.md b/cmd/config-validator/README.md
index b1ae4d4..cfd0c52 100644
--- a/cmd/config-validator/README.md
+++ b/cmd/config-validator/README.md
@@ -1,6 +1,6 @@
 # config-validator
 
-Command-line tool for validating and testing examples-copier workflow configurations.
+Command-line tool for validating and testing github-copier workflow configurations.
 
 > **Note:** This tool validates individual workflow config files. It does not validate main config files. Main config validation is built into the application itself.
 
@@ -15,7 +15,7 @@ The `config-validator` tool helps you:
 ## Installation
 
 ```bash
-cd examples-copier
+cd github-copier
 go build -o config-validator ./cmd/config-validator
 ```
 
diff --git a/cmd/config-validator/main.go b/cmd/config-validator/main.go
index 866cdcb..9c3eee7 100644
--- a/cmd/config-validator/main.go
+++ b/cmd/config-validator/main.go
@@ -6,8 +6,8 @@ import (
 	"os"
 	"strings"
 
-	"github.com/mongodb/code-example-tooling/code-copier/services"
-	"github.com/mongodb/code-example-tooling/code-copier/types"
+	"github.com/grove-platform/github-copier/services"
+	"github.com/grove-platform/github-copier/types"
 )
 
 func main() {
@@ -37,7 +37,7 @@ func main() {
 
 	switch os.Args[1] {
 	case "validate":
-		validateCmd.Parse(os.Args[2:])
+		_ = validateCmd.Parse(os.Args[2:])
 		if *validateFile == "" {
 			fmt.Println("Error: -config is required")
 			validateCmd.Usage()
@@ -46,7 +46,7 @@ func main() {
 		validateConfig(*validateFile, *validateVerbose)
 
 	case "test-pattern":
-		testPatternCmd.Parse(os.Args[2:])
+		_ = testPatternCmd.Parse(os.Args[2:])
 		if *pattern == "" || *filePath == "" {
 			fmt.Println("Error: -pattern and -file are required")
 			testPatternCmd.Usage()
@@ -55,7 +55,7 @@ func main() {
 		testPattern(*patternType, *pattern, *filePath)
 
 	case "test-transform":
-		testTransformCmd.Parse(os.Args[2:])
+		_ = testTransformCmd.Parse(os.Args[2:])
 		if *transformSource == "" || *transformTemplate == "" {
 			fmt.Println("Error: -source and -template are required")
 			testTransformCmd.Usage()
@@ -64,7 +64,7 @@ func main() {
 		testTransform(*transformSource, *transformTemplate, *transformVars)
 
 	case "init":
-		initCmd.Parse(os.Args[2:])
+		_ = initCmd.Parse(os.Args[2:])
 		initConfig(*initTemplate, *initOutput)
 
 	default:
diff --git a/cmd/test-webhook/README.md b/cmd/test-webhook/README.md
index 69db911..10070bf 100644
--- a/cmd/test-webhook/README.md
+++ b/cmd/test-webhook/README.md
@@ -1,6 +1,6 @@
 # test-webhook
 
-Command-line tool for testing the examples-copier webhook endpoint with example or real PR data.
+Command-line tool for testing the github-copier webhook endpoint with example or real PR data.
 
 ## Overview
 
@@ -14,7 +14,7 @@ The `test-webhook` tool helps you:
 ## Installation
 
 ```bash
-cd examples-copier
+cd github-copier
 go build -o test-webhook ./cmd/test-webhook
 ```
 
@@ -37,10 +37,10 @@ Send a pre-made example payload to the webhook endpoint.
 
 ```bash
 # Use example payload
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 
 # Use custom URL
-./test-webhook -payload test-payloads/example-pr-merged.json \
+./test-webhook -payload testdata/example-pr-merged.json \
   -url http://localhost:8080/webhook
 ```
 
@@ -48,7 +48,7 @@ Send a pre-made example payload to the webhook endpoint.
 ```
 Testing webhook with example payload...
 
-✓ Loaded payload from test-payloads/example-pr-merged.json
+✓ Loaded payload from testdata/example-pr-merged.json
 ✓ Response: 200 OK
 ✓ Webhook sent successfully
 
@@ -111,7 +111,7 @@ Test your configuration locally before deploying:
 DRY_RUN=true make run-local-quick
 
 # 2. In another terminal, send test webhook
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 
 # 3. Check logs
 tail -f logs/app.log
@@ -139,10 +139,10 @@ Verify files are copied to correct locations:
 
 ```bash
 # 1. Start app in dry-run mode
-DRY_RUN=true ./examples-copier &
+DRY_RUN=true ./github-copier &
 
 # 2. Send test webhook
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 
 # 3. Check logs for transformed paths
 grep "transformed path" logs/app.log
@@ -155,10 +155,10 @@ Test Slack integration:
 ```bash
 # 1. Start app with Slack enabled
 export SLACK_WEBHOOK_URL="https://hooks.slack.com/services/..."
-./examples-copier &
+./github-copier &
 
 # 2. Send test webhook
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 
 # 3. Check Slack channel for notification
 ```
@@ -170,10 +170,10 @@ Debug webhook processing:
 ```bash
 # 1. Enable debug logging
 export LOG_LEVEL=debug
-./examples-copier &
+./github-copier &
 
 # 2. Send test webhook
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 
 # 3. Review detailed logs
 grep "DEBUG" logs/app.log
@@ -181,7 +181,7 @@ grep "DEBUG" logs/app.log
 
 ## Example Payloads
 
-The `test-payloads/` directory contains example webhook payloads:
+The `testdata/` directory contains example webhook payloads:
 
 ### example-pr-merged.json
 
@@ -192,7 +192,7 @@ A complete merged PR payload with:
 
 **Usage:**
 ```bash
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 ```
 
 ### Creating Custom Payloads
@@ -201,13 +201,13 @@ Create custom payloads for specific test scenarios:
 
 ```bash
 # Copy example
-cp test-payloads/example-pr-merged.json test-payloads/my-test.json
+cp testdata/example-pr-merged.json testdata/my-test.json
 
 # Edit to match your test case
-vim test-payloads/my-test.json
+vim testdata/my-test.json
 
 # Test with custom payload
-./test-webhook -payload test-payloads/my-test.json
+./test-webhook -payload testdata/my-test.json
 ```
 
 **Example custom payload:**
@@ -234,10 +234,10 @@ vim test-payloads/my-test.json
 
 ```bash
 # 1. Start app in dry-run mode
-DRY_RUN=true ./examples-copier &
+DRY_RUN=true ./github-copier &
 
 # 2. Test with example payload
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 
 # 3. Check metrics
 curl http://localhost:8080/metrics | jq
@@ -274,7 +274,7 @@ Response: 401 Unauthorized
 **Solution:** Disable webhook signature verification for testing:
 ```bash
 unset WEBHOOK_SECRET
-./examples-copier &
+./github-copier &
 ```
 
 ### 404 Not Found
@@ -311,7 +311,7 @@ Error: invalid JSON payload
 
 **Solution:** Validate your JSON:
 ```bash
-cat test-payloads/my-test.json | jq
+cat testdata/my-test.json | jq
 ```
 
 ## Advanced Usage
@@ -344,12 +344,12 @@ cat > run-tests.sh << 'EOF'
 set -e
 
 echo "Starting app..."
-DRY_RUN=true ./examples-copier &
+DRY_RUN=true ./github-copier &
 APP_PID=$!
 sleep 2
 
 echo "Running tests..."
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 
 echo "Checking metrics..."
 curl -s http://localhost:8080/metrics | jq '.files.matched'
@@ -385,14 +385,14 @@ jobs:
       
       - name: Build
         run: |
-          go build -o examples-copier .
+          go build -o github-copier .
           go build -o test-webhook ./cmd/test-webhook
       
       - name: Test
         run: |
-          DRY_RUN=true ./examples-copier &
+          DRY_RUN=true ./github-copier &
           sleep 2
-          ./test-webhook -payload test-payloads/example-pr-merged.json
+          ./test-webhook -payload testdata/example-pr-merged.json
 ```
 
 ## Exit Codes
@@ -404,6 +404,6 @@ jobs:
 
 - [Webhook Testing Guide](../../docs/WEBHOOK-TESTING.md) - Comprehensive testing guide
 - [Local Testing](../../docs/LOCAL-TESTING.md) - Local development
-- [Test Payloads](../../test-payloads/README.md) - Example payloads
+- [Test Payloads](../../testdata/README.md) - Example payloads
 - [Quick Reference](../../QUICK-REFERENCE.md) - All commands
 
diff --git a/configs/README.md b/configs/README.md
index 068e6a1..5a4ab16 100644
--- a/configs/README.md
+++ b/configs/README.md
@@ -142,7 +142,7 @@ REPO_OWNER: "mongodb"
 cp configs/env.yaml.production env-cloudrun.yaml
 # Remove the 'env_variables:' wrapper
 # Edit env-cloudrun.yaml with your values
-gcloud run deploy examples-copier --source . --env-vars-file=env-cloudrun.yaml
+gcloud run deploy github-copier --source . --env-vars-file=env-cloudrun.yaml
 ```
 
 **Best for:** Cost-effective, scales to zero, serverless
@@ -299,7 +299,7 @@ diff configs/env.yaml.production configs/env.yaml.example
 ## File Locations
 
 ```
-examples-copier/
+github-copier/
 ├── configs/
 │   ├── env.yaml.example          # ← Complete reference (all variables)
 │   ├── env.yaml.production       # ← Production template (essential only)
diff --git a/configs/copier-config-examples/SOURCE-REPO-README.md b/configs/copier-config-examples/SOURCE-REPO-README.md
index 0e1ef61..b48b54c 100644
--- a/configs/copier-config-examples/SOURCE-REPO-README.md
+++ b/configs/copier-config-examples/SOURCE-REPO-README.md
@@ -8,7 +8,7 @@ This directory contains workflow configurations for automatically copying code e
 
 **What do I need to know?**
 1. When you **merge a PR** in this repo, the copier automatically runs
-2. Files are **matched against patterns** in `.copier/workflows.yaml`
+2. Files are **matched against patterns** in `.copier/config.yaml`
 3. Matched files are **copied to destination repositories**
 4. A **PR is created** in each destination repository (usually)
 5. Someone needs to **review and merge** the destination PRs (unless auto-merge is enabled)
@@ -31,7 +31,7 @@ gcloud app logs read --limit=100 | grep "your-repo-name"
 
 ### File Location
 
-Place your workflow configuration at: `.copier/workflows.yaml`
+Place your workflow configuration at: `.copier/config.yaml`
 
 ### Basic Workflow Structure
 
@@ -51,7 +51,7 @@ workflows:
 
 **All file paths in transformations are relative to the repository root**, not to the config file location.
 
-Even though your config is at `.copier/workflows.yaml`, patterns and paths are matched against the full repository path:
+Even though your config is at `.copier/config.yaml`, patterns and paths are matched against the full repository path:
 
 ```yaml
 # ✅ Correct - paths from repository root
@@ -69,7 +69,7 @@ transformations:
 
 ## Adding a New Workflow
 
-1. **Edit `.copier/workflows.yaml`** in your repository
+1. **Edit `.copier/config.yaml`** in your repository
 
 2. **Add a new workflow entry:**
 
@@ -89,7 +89,7 @@ workflows:
 
 ## Modifying an Existing Workflow
 
-Simply edit the workflow in `.copier/workflows.yaml` and commit your changes. The updated configuration will be used for the next PR merge.
+Simply edit the workflow in `.copier/config.yaml` and commit your changes. The updated configuration will be used for the next PR merge.
 
 ## Common Transformation Types
 
@@ -262,7 +262,7 @@ Before committing, you can validate your configuration:
 
 ```bash
 # Validate syntax
-./config-validator validate -config .copier/workflows.yaml
+./config-validator validate -config .copier/config.yaml
 
 # Test a pattern match
 ./config-validator test-pattern \
@@ -277,7 +277,7 @@ Before committing, you can validate your configuration:
 
 1. **You merge a PR** in this repository
 2. **GitHub sends a webhook** to the copier application
-3. **Copier loads your workflows** from `.copier/workflows.yaml`
+3. **Copier loads your workflows** from `.copier/config.yaml`
 4. **Files are matched** against transformation patterns
 5. **Files are copied** to destination repositories
 6. **PRs are created** in destination repositories (or committed directly)
@@ -401,16 +401,16 @@ The deprecation file is stored in **this repository** (source):
 
 ## Need Help?
 
-- **Full Documentation**: [Code Example Tooling Repository](https://github.com/mongodb/code-example-tooling)
-- **Configuration Examples**: See `examples-copier/configs/copier-config-examples/`
-- **Pattern Matching Guide**: See `examples-copier/docs/PATTERN-MATCHING-GUIDE.md`
-- **Main Config Architecture**: See `examples-copier/configs/copier-config-examples/MAIN-CONFIG-README.md`
-- **Deprecation Tracking**: See `examples-copier/docs/DEPRECATION-TRACKING-EXPLAINED.md`
+- **Full Documentation**: [Code Example Tooling Repository](https://github.com/grove-platform/github-copier)
+- **Configuration Examples**: See `github-copier/configs/copier-config-examples/`
+- **Pattern Matching Guide**: See `github-copier/docs/PATTERN-MATCHING-GUIDE.md`
+- **Main Config Architecture**: See `github-copier/configs/copier-config-examples/MAIN-CONFIG-README.md`
+- **Deprecation Tracking**: See `github-copier/docs/DEPRECATION-TRACKING-EXPLAINED.md`
 
 ## Example: Complete Workflow
 
 ```yaml
-# .copier/workflows.yaml
+# .copier/config.yaml
 
 defaults:
   commit_strategy:
@@ -450,7 +450,7 @@ workflows:
 1. Was it a merged PR? (not just closed)
 2. Do the changed files match your transformation patterns?
 3. Check the copier logs (see below)
-4. Verify `.copier/workflows.yaml` is valid YAML
+4. Verify `.copier/config.yaml` is valid YAML
 
 ### How do I view the logs?
 
@@ -469,7 +469,7 @@ gcloud app logs read --limit=200 | grep "your-repo-name"
 
 ```bash
 # Validate YAML syntax
-./config-validator validate -config .copier/workflows.yaml
+./config-validator validate -config .copier/config.yaml
 
 # Test a pattern match
 ./config-validator test-pattern \
@@ -506,5 +506,5 @@ workflows:
 
 ## Questions?
 
-Contact the Developer Docs team or open an issue in the [code-example-tooling repository](https://github.com/mongodb/code-example-tooling/issues).
+Contact the Developer Docs team or open an issue in the [github-copier repository](https://github.com/grove-platform/github-copier/issues).
 
diff --git a/docs/ARCHITECTURE.md b/docs/ARCHITECTURE.md
index 0098d30..32c29cb 100644
--- a/docs/ARCHITECTURE.md
+++ b/docs/ARCHITECTURE.md
@@ -1,6 +1,6 @@
-# Examples Copier Architecture
+# GitHub Copier Architecture
 
-This document describes the architecture and design of the examples-copier application, including its core components, main config system, pattern matching, configuration management, deprecation tracking, and operational features.
+This document describes the architecture and design of the github-copier application, including its core components, main config system, pattern matching, configuration management, deprecation tracking, and operational features.
 
 ## Core Architecture
 
diff --git a/docs/DEPLOYMENT.md b/docs/DEPLOYMENT.md
index 6717bba..b7d312d 100644
--- a/docs/DEPLOYMENT.md
+++ b/docs/DEPLOYMENT.md
@@ -69,7 +69,7 @@ gcloud config get-value project
 ┌─────────────────────────────────────────────────────────────┐
 │              Google Cloud Run                               │
 │  ┌──────────────────────────────────────────────────────┐   │
-│  │  examples-copier Service (Container)                 │   │
+│  │  github-copier Service (Container)                 │   │
 │  │  - Receives webhook                                  │   │
 │  │  - Validates signature                               │   │
 │  │  - Loads config from source repo                     │   │
@@ -108,7 +108,7 @@ This application uses **Google Cloud Run** (serverless containers):
 
 **Deployment:**
 ```bash
-gcloud run deploy examples-copier \
+gcloud run deploy github-copier \
   --source . \
   --region us-central1 \
   --env-vars-file=env-cloudrun.yaml
@@ -191,7 +191,7 @@ gcloud secrets add-iam-policy-binding mongo-uri \
 
 **Or use the provided script:**
 ```bash
-cd examples-copier
+cd github-copier
 ./scripts/grant-secret-access.sh
 ```
 
@@ -215,7 +215,7 @@ gcloud secrets get-iam-policy CODE_COPIER_PEM
 The `env-cloudrun.yaml` file contains environment variables for Cloud Run deployment.
 
 ```bash
-cd examples-copier
+cd github-copier
 
 # Copy from example or create new
 cp env.yaml env-cloudrun.yaml
@@ -335,7 +335,7 @@ services.LoadMongoURI(config)       // Loads from Secret Manager
 The simplest way to deploy is using the provided script:
 
 ```bash
-cd examples-copier
+cd github-copier
 
 # Deploy to default region (us-central1)
 ./scripts/deploy-cloudrun.sh
@@ -356,9 +356,9 @@ The script will:
 If you prefer to run the command directly:
 
 ```bash
-cd examples-copier
+cd github-copier
 
-gcloud run deploy examples-copier \
+gcloud run deploy github-copier \
   --source . \
   --region us-central1 \
   --env-vars-file=env-cloudrun.yaml \
@@ -390,16 +390,16 @@ gcloud run deploy examples-copier \
 gcloud run services list --region=us-central1
 
 # Get service URL
-SERVICE_URL=$(gcloud run services describe examples-copier \
+SERVICE_URL=$(gcloud run services describe github-copier \
   --region=us-central1 \
   --format="value(status.url)")
 echo "Service URL: ${SERVICE_URL}"
 
 # View logs
-gcloud run services logs read examples-copier --region=us-central1 --limit=50
+gcloud run services logs read github-copier --region=us-central1 --limit=50
 
 # Or tail logs in real-time
-gcloud run services logs tail examples-copier --region=us-central1
+gcloud run services logs tail github-copier --region=us-central1
 ```
 
 ### Test Health Endpoint
@@ -608,7 +608,7 @@ echo -n "mongodb+srv://..." | gcloud secrets create mongo-uri \
 
 ```bash
 # Run the grant script
-cd examples-copier
+cd github-copier
 ./scripts/grant-secret-access.sh
 ```
 
@@ -641,7 +641,7 @@ gcloud secrets get-iam-policy mongo-uri | grep @appspot
 ### ☐ 5. Create env.yaml
 
 ```bash
-cd examples-copier
+cd github-copier
 
 # Copy from template
 cp configs/env.yaml.production env.yaml
@@ -698,7 +698,7 @@ env: flex
 ### ☐ 8. Deploy to Cloud Run
 
 ```bash
-cd examples-copier
+cd github-copier
 
 # Deploy using the deployment script
 ./scripts/deploy-cloudrun.sh
diff --git a/docs/DEPRECATION-TRACKING-EXPLAINED.md b/docs/DEPRECATION-TRACKING-EXPLAINED.md
index c2d22bc..a5947f8 100644
--- a/docs/DEPRECATION-TRACKING-EXPLAINED.md
+++ b/docs/DEPRECATION-TRACKING-EXPLAINED.md
@@ -218,7 +218,7 @@ After cleanup, remove the entry from `deprecated_examples.json`.
 In dry-run mode, deprecation tracking is **simulated**:
 
 ```bash
-DRY_RUN=true ./examples-copier
+DRY_RUN=true ./github-copier
 ```
 
 **Output:**
diff --git a/docs/FAQ.md b/docs/FAQ.md
index e26c4c5..2b8a479 100644
--- a/docs/FAQ.md
+++ b/docs/FAQ.md
@@ -1,14 +1,14 @@
 # Frequently Asked Questions (FAQ)
 
-Common questions about the examples-copier application.
+Common questions about the github-copier application.
 
 ## General Questions
 
-### What is examples-copier?
+### What is github-copier?
 
-Examples-copier is a GitHub app that automatically copies code examples and files from a source repository to one or more target repositories when pull requests are merged. It features advanced pattern matching, path transformations, and audit logging.
+The GitHub copier is a GitHub app that automatically copies code examples and files from a source repository to one or more target repositories when pull requests are merged. It features advanced pattern matching, path transformations, and audit logging.
 
-### Why use examples-copier?
+### Why use github-copier?
 
 - **Automate file synchronization** between repositories
 - **Maintain consistency** across multiple documentation repos
@@ -74,7 +74,7 @@ Yes. A file can match multiple workflows and be copied to multiple targets. This
 
 **Workflow configs:** Store in `.copier/workflows/config.yaml` in source repositories, or reference them from the main config.
 
-**For local testing:** Store config files in the examples-copier directory and set appropriate environment variables.
+**For local testing:** Store config files in the github-copier directory and set appropriate environment variables.
 
 ## Pattern Matching
 
@@ -204,7 +204,7 @@ The app uses Google Cloud Secret Manager for storing GitHub credentials. You cou
 
 2. Send a test webhook:
    ```bash
-   ./test-webhook -payload test-payloads/example-pr-merged.json
+   ./test-webhook -payload testdata/example-pr-merged.json
    ```
 
 See [Local Testing](LOCAL-TESTING.md) for details.
diff --git a/docs/LOCAL-TESTING.md b/docs/LOCAL-TESTING.md
index 06ee239..0c4ee64 100644
--- a/docs/LOCAL-TESTING.md
+++ b/docs/LOCAL-TESTING.md
@@ -1,6 +1,6 @@
 # Local Testing Guide
 
-This guide explains how to run and test the examples-copier application locally without requiring Google Cloud or MongoDB.
+This guide explains how to run and test the github-copier application locally without requiring Google Cloud or MongoDB.
 
 ## Quick Start
 
@@ -18,7 +18,7 @@ make run-local
 
 ```bash
 # One-liner for quick testing
-COPIER_DISABLE_CLOUD_LOGGING=true DRY_RUN=true ./examples-copier
+COPIER_DISABLE_CLOUD_LOGGING=true DRY_RUN=true ./github-copier
 ```
 
 ### Option 3: Use Makefile
@@ -93,7 +93,7 @@ make test-webhook-example
 
 # Or send webhook manually with secret
 export WEBHOOK_SECRET=$(gcloud secrets versions access latest --secret=webhook-secret)
-./test-webhook -payload test-payloads/example-pr-merged.json -secret "$WEBHOOK_SECRET"
+./test-webhook -payload testdata/example-pr-merged.json -secret "$WEBHOOK_SECRET"
 
 # Or test with real PR
 export GITHUB_TOKEN=ghp_...
@@ -155,7 +155,7 @@ nano .copier/workflows/main.yaml
 make run-local
 
 # 4. Send test webhook
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 
 # 5. Check logs to verify changes work
 ```
@@ -311,7 +311,7 @@ AUDIT_COLLECTION=audit_events
 **Solution:**
 ```bash
 # Disable cloud logging for local testing
-COPIER_DISABLE_CLOUD_LOGGING=true ./examples-copier
+COPIER_DISABLE_CLOUD_LOGGING=true ./github-copier
 ```
 
 ### Error: "connection refused" when sending webhook
@@ -324,12 +324,12 @@ COPIER_DISABLE_CLOUD_LOGGING=true ./examples-copier
 make run-local-quick
 
 # Terminal 2: In a NEW terminal window, send the webhook
-cd examples-copier
+cd github-copier
 make test-webhook-example
 
 # Or manually:
 export WEBHOOK_SECRET=$(gcloud secrets versions access latest --secret=webhook-secret)
-./test-webhook -payload test-payloads/example-pr-merged.json -secret "$WEBHOOK_SECRET"
+./test-webhook -payload testdata/example-pr-merged.json -secret "$WEBHOOK_SECRET"
 ```
 
 **Note:** The `make test-webhook-example` command requires the server to be running in a separate terminal. You cannot run both commands in the same terminal unless you background the server process.
@@ -384,7 +384,7 @@ make build
 make run-local
 
 # 5. In Terminal 2, test with example payload
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 
 # 6. Check metrics
 curl http://localhost:8080/metrics | jq
@@ -438,7 +438,7 @@ make test-webhook-example
 
 # Or test manually with webhook secret
 export WEBHOOK_SECRET=$(gcloud secrets versions access latest --secret=webhook-secret)
-./test-webhook -payload test-payloads/example-pr-merged.json -secret "$WEBHOOK_SECRET"
+./test-webhook -payload testdata/example-pr-merged.json -secret "$WEBHOOK_SECRET"
 
 # Test with real PR
 export GITHUB_TOKEN=ghp_...
diff --git a/docs/PATTERN-MATCHING-GUIDE.md b/docs/PATTERN-MATCHING-GUIDE.md
index 18fe427..59bf661 100644
--- a/docs/PATTERN-MATCHING-GUIDE.md
+++ b/docs/PATTERN-MATCHING-GUIDE.md
@@ -1,6 +1,6 @@
 # Pattern Matching Guide
 
-Complete guide to pattern matching and path transformation in the examples-copier.
+Complete guide to pattern matching and path transformation in the github-copier.
 
 ## Table of Contents
 
@@ -18,7 +18,7 @@ Complete guide to pattern matching and path transformation in the examples-copie
 
 ## Overview
 
-The examples-copier uses a powerful pattern matching system to:
+The github-copier uses a powerful pattern matching system to:
 1. **Match files** from merged PRs based on their paths
 2. **Extract variables** from file paths (e.g., language, category)
 3. **Transform paths** to determine where files should be copied
diff --git a/docs/SLACK-NOTIFICATIONS.md b/docs/SLACK-NOTIFICATIONS.md
index ed35e19..50fef96 100644
--- a/docs/SLACK-NOTIFICATIONS.md
+++ b/docs/SLACK-NOTIFICATIONS.md
@@ -1,6 +1,6 @@
 # Slack Notifications
 
-The examples-copier supports sending notifications to Slack when PRs are processed, files are copied, or errors occur.
+The github-copier supports sending notifications to Slack when PRs are processed, files are copied, or errors occur.
 
 ## Features
 
@@ -47,7 +47,7 @@ CONFIG_FILE=copier-config.yaml \
 make run-local-quick
 
 # Send a test webhook
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 ```
 
 You should see a notification in your Slack channel!
@@ -217,7 +217,7 @@ export SLACK_WEBHOOK_URL="https://hooks.slack.com/services/..."
 CONFIG_FILE=copier-config.yaml make run-local-quick
 
 # Send test webhook
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 ```
 
 ### Test with Real PR
@@ -283,7 +283,7 @@ To reduce notification frequency:
 Add environment variables to your Cloud Run service:
 
 ```bash
-gcloud run services update examples-copier \
+gcloud run services update github-copier \
   --set-env-vars="SLACK_WEBHOOK_URL=https://hooks.slack.com/services/..." \
   --set-env-vars="SLACK_CHANNEL=#code-examples"
 ```
@@ -294,7 +294,7 @@ Add to your `docker-compose.yml`:
 
 ```yaml
 services:
-  examples-copier:
+  github-copier:
     environment:
       - SLACK_WEBHOOK_URL=https://hooks.slack.com/services/...
       - SLACK_CHANNEL=#code-examples
diff --git a/docs/TROUBLESHOOTING.md b/docs/TROUBLESHOOTING.md
index 254f703..f2cc55d 100644
--- a/docs/TROUBLESHOOTING.md
+++ b/docs/TROUBLESHOOTING.md
@@ -1,6 +1,6 @@
 # Troubleshooting Guide
 
-Common issues and solutions for the examples-copier application.
+Common issues and solutions for the github-copier application.
 
 ## Table of Contents
 
@@ -38,7 +38,7 @@ Common issues and solutions for the examples-copier application.
    cp copier-config.yaml /path/to/source-repo/copier-config.yaml
    cd /path/to/source-repo
    git add copier-config.yaml
-   git commit -m "Add examples-copier config"
+   git commit -m "Add github-copier config"
    git push
    ```
 
@@ -221,7 +221,7 @@ pattern: "^examples/(?P<lang>[^/]+)/(?P<file>.+)$"
 
 3. **Test with dry-run mode:**
    ```bash
-   DRY_RUN=true ./examples-copier
+   DRY_RUN=true ./github-copier
    ```
 
 ### No Response from Webhook
@@ -241,7 +241,7 @@ pattern: "^examples/(?P<lang>[^/]+)/(?P<file>.+)$"
 
 3. **Test with curl:**
    ```bash
-   ./test-webhook -payload test-payloads/example-pr-merged.json
+   ./test-webhook -payload testdata/example-pr-merged.json
    ```
 
 ## Deployment Issues
@@ -256,7 +256,7 @@ pattern: "^examples/(?P<lang>[^/]+)/(?P<file>.+)$"
 **Solution:** Disable cloud logging for local testing:
 ```bash
 export COPIER_DISABLE_CLOUD_LOGGING=true
-./examples-copier
+./github-copier
 ```
 
 ### MongoDB Connection Failed
@@ -305,7 +305,7 @@ export COPIER_DISABLE_CLOUD_LOGGING=true
 
 3. **For testing, use dry-run mode:**
    ```bash
-   DRY_RUN=true ./examples-copier
+   DRY_RUN=true ./github-copier
    ```
 
 ## Slack Notification Issues
@@ -394,7 +394,7 @@ export SLACK_CHANNEL="#your-channel"
 1. **Check for memory leaks:**
    ```bash
    # Monitor memory usage
-   top -p $(pgrep examples-copier)
+   top -p $(pgrep github-copier)
    ```
 
 2. **Common causes:**
@@ -413,7 +413,7 @@ export SLACK_CHANNEL="#your-channel"
 
 ```bash
 export LOG_LEVEL=debug
-./examples-copier
+./github-copier
 ```
 
 ### Check Health Endpoint
@@ -455,8 +455,8 @@ curl http://localhost:8080/metrics | jq
 ### Test with Dry-Run Mode
 
 ```bash
-DRY_RUN=true ./examples-copier &
-./test-webhook -payload test-payloads/example-pr-merged.json
+DRY_RUN=true ./github-copier &
+./test-webhook -payload testdata/example-pr-merged.json
 ```
 
 ### Check Audit Logs
diff --git a/docs/WEBHOOK-TESTING.md b/docs/WEBHOOK-TESTING.md
index 00a0d7e..5042e90 100644
--- a/docs/WEBHOOK-TESTING.md
+++ b/docs/WEBHOOK-TESTING.md
@@ -1,6 +1,6 @@
 # Webhook Testing Guide
 
-This guide explains how to test the examples-copier application with webhooks using real PR data or example payloads.
+This guide explains how to test the github-copier application with webhooks using real PR data or example payloads.
 
 ## Quick Start
 
@@ -18,10 +18,10 @@ go build -o test-webhook ./cmd/test-webhook
 
 ```bash
 # Send example payload to local server
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 
 # See payload without sending
-./test-webhook -payload test-payloads/example-pr-merged.json -dry-run
+./test-webhook -payload testdata/example-pr-merged.json -dry-run
 ```
 
 ### 3. Test with Real PR Data
@@ -45,10 +45,10 @@ Test your configuration changes locally before deploying:
 
 ```bash
 # Terminal 1: Start app in dry-run mode
-DRY_RUN=true ./examples-copier
+DRY_RUN=true ./github-copier
 
 # Terminal 2: Send test webhook
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 
 # Check Terminal 1 for processing logs
 ```
@@ -125,7 +125,7 @@ cat > test-go-only.json <<EOF
 EOF
 
 # Test
-DRY_RUN=true ./examples-copier &
+DRY_RUN=true ./github-copier &
 ./test-webhook -payload test-go-only.json
 ```
 
@@ -231,7 +231,7 @@ chmod +x scripts/test-with-pr.sh
 
 ### Complete Payload
 
-See `test-payloads/example-pr-merged.json` for a complete example with:
+See `testdata/example-pr-merged.json` for a complete example with:
 - Multiple file changes (added, modified, removed)
 - Full PR metadata
 - Repository information
@@ -425,14 +425,14 @@ Add webhook testing to your CI pipeline:
 - name: Test webhook processing
   run: |
     # Start app in background
-    DRY_RUN=true ./examples-copier &
+    DRY_RUN=true ./github-copier &
     APP_PID=$!
     
     # Wait for app to start
     sleep 5
     
     # Run webhook tests
-    ./test-webhook -payload test-payloads/example-pr-merged.json
+    ./test-webhook -payload testdata/example-pr-merged.json
     
     # Stop app
     kill $APP_PID
diff --git a/env-cloudrun.yaml b/env-cloudrun.yaml
new file mode 100644
index 0000000..a255f63
--- /dev/null
+++ b/env-cloudrun.yaml
@@ -0,0 +1,36 @@
+# Cloud Run environment variables
+# Format: KEY: "VALUE" (no env_variables wrapper needed)
+# Note: PORT is automatically set by Cloud Run, don't override it
+
+# GitHub Configuration
+GITHUB_APP_ID: "1166559"
+INSTALLATION_ID: "95537167" # grove-platform
+
+# Config Repository (where main config file is stored)
+CONFIG_REPO_OWNER: "grove-platform"
+CONFIG_REPO_NAME: "github-copier"
+CONFIG_REPO_BRANCH: "main"
+
+# Secret Manager References
+GITHUB_APP_PRIVATE_KEY_SECRET_NAME: "projects/1054147886816/secrets/CODE_COPIER_PEM/versions/latest"
+WEBHOOK_SECRET_NAME: "projects/1054147886816/secrets/webhook-secret/versions/latest"
+MONGO_URI_SECRET_NAME: "projects/1054147886816/secrets/mongo-uri/versions/latest"
+
+# Application Settings
+WEBSERVER_PATH: "/events"
+MAIN_CONFIG_FILE: ".copier/main.yaml"
+USE_MAIN_CONFIG: "true"
+DEPRECATION_FILE: "deprecated_examples.json"
+
+# Committer Information
+COMMITTER_NAME: "GitHub Copier App"
+COMMITTER_EMAIL: "bot@mongodb.com"
+
+# Google Cloud Configuration
+GOOGLE_CLOUD_PROJECT_ID: "github-copy-code-examples"
+COPIER_LOG_NAME: "code-copier-log"
+
+# Feature Flags
+AUDIT_ENABLED: "false"
+METRICS_ENABLED: "true"
+
diff --git a/go.mod b/go.mod
index aeb69fa..3a6d555 100644
--- a/go.mod
+++ b/go.mod
@@ -1,4 +1,4 @@
-module github.com/mongodb/code-example-tooling/code-copier
+module github.com/grove-platform/github-copier
 
 go 1.24.0
 
diff --git a/scripts/README.md b/scripts/README.md
index 6233af8..c6a3c01 100644
--- a/scripts/README.md
+++ b/scripts/README.md
@@ -1,12 +1,12 @@
 # Helper Scripts
 
-Collection of helper scripts for testing and running the examples-copier application.
+Collection of helper scripts for testing and running the github-copier application.
 
 ## Scripts
 
 ### run-local.sh
 
-Start the examples-copier application locally with proper environment configuration.
+Start the github-copier application locally with proper environment configuration.
 
 **Usage:**
 ```bash
@@ -25,7 +25,7 @@ Start the examples-copier application locally with proper environment configurat
 ./scripts/run-local.sh
 
 # In another terminal, test it
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 ```
 
 **Environment:**
@@ -61,7 +61,7 @@ Send a test webhook and check the metrics.
 ```
 Testing webhook with example payload...
 
-✓ Loaded payload from test-payloads/example-pr-merged.json
+✓ Loaded payload from testdata/example-pr-merged.json
 ✓ Response: 200 OK
 ✓ Webhook sent successfully
 
diff --git a/scripts/integration-test.sh b/scripts/integration-test.sh
new file mode 100755
index 0000000..1914487
--- /dev/null
+++ b/scripts/integration-test.sh
@@ -0,0 +1,142 @@
+#!/bin/bash
+# Integration test script for github-copier
+# Sends test webhook payload to locally running app
+#
+# Usage:
+#   ./scripts/integration-test.sh webhook   # Send test webhook
+#   ./scripts/integration-test.sh verify    # Check dest repos
+#   ./scripts/integration-test.sh full      # Both + wait
+#
+# Environment:
+#   APP_URL         - App URL (default: http://localhost:8080)
+#   WEBHOOK_SECRET  - Webhook secret (default: reads from .env.test)
+#   PAYLOAD_FILE    - Payload file (default: testdata/test-pr-merged.json)
+
+set -e
+
+# Load webhook secret from .env.test if it exists and WEBHOOK_SECRET not set
+if [[ -z "$WEBHOOK_SECRET" && -f ".env.test" ]]; then
+    WEBHOOK_SECRET=$(grep -E "^WEBHOOK_SECRET=" .env.test | cut -d'=' -f2- | tr -d '"' | tr -d "'")
+fi
+
+# Configuration
+APP_URL="${APP_URL:-http://localhost:8080}"
+WEBHOOK_SECRET="${WEBHOOK_SECRET:-test-secret}"
+PAYLOAD_FILE="${PAYLOAD_FILE:-testdata/test-pr-merged.json}"
+
+# Colors
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+NC='\033[0m' # No Color
+
+log_info() { echo -e "${GREEN}[INFO]${NC} $1"; }
+log_warn() { echo -e "${YELLOW}[WARN]${NC} $1"; }
+log_error() { echo -e "${RED}[ERROR]${NC} $1"; }
+
+# Check if app is running
+check_app() {
+    log_info "Checking if app is running at $APP_URL..."
+    if curl -s "$APP_URL/health" > /dev/null 2>&1; then
+        log_info "App is running"
+        return 0
+    else
+        log_error "App is not running at $APP_URL"
+        log_info "Start the app with: go run app.go"
+        return 1
+    fi
+}
+
+# Generate HMAC signature for webhook
+generate_signature() {
+    local payload="$1"
+    echo -n "$payload" | openssl dgst -sha256 -hmac "$WEBHOOK_SECRET" | sed 's/^.* //'
+}
+
+# Send webhook payload
+send_webhook() {
+    local payload_file="$1"
+    
+    if [[ ! -f "$payload_file" ]]; then
+        log_error "Payload file not found: $payload_file"
+        return 1
+    fi
+    
+    local payload=$(cat "$payload_file")
+    local signature="sha256=$(generate_signature "$payload")"
+    
+    log_info "Sending webhook payload from $payload_file..."
+    log_info "Signature: $signature"
+    
+    response=$(curl -s -w "\n%{http_code}" \
+        -X POST "$APP_URL/webhook" \
+        -H "Content-Type: application/json" \
+        -H "X-GitHub-Event: pull_request" \
+        -H "X-Hub-Signature-256: $signature" \
+        -d "$payload")
+    
+    http_code=$(echo "$response" | tail -n1)
+    body=$(echo "$response" | sed '$d')
+    
+    if [[ "$http_code" == "200" ]]; then
+        log_info "Webhook accepted (HTTP $http_code)"
+        echo "$body"
+        return 0
+    else
+        log_error "Webhook rejected (HTTP $http_code)"
+        echo "$body"
+        return 1
+    fi
+}
+
+# Verify files in destination repo (requires gh CLI)
+verify_dest_repo() {
+    local repo="$1"
+    local path="$2"
+    
+    log_info "Checking $repo for $path..."
+    if gh api "repos/$repo/contents/$path" > /dev/null 2>&1; then
+        log_info "✓ Found $path in $repo"
+        return 0
+    else
+        log_warn "✗ Not found: $path in $repo"
+        return 1
+    fi
+}
+
+# Main
+main() {
+    echo "=========================================="
+    echo "GitHub Copier Integration Test"
+    echo "=========================================="
+    
+    case "${1:-webhook}" in
+        webhook)
+            check_app || exit 1
+            send_webhook "$PAYLOAD_FILE"
+            ;;
+        verify)
+            log_info "Verifying destination repos..."
+            verify_dest_repo "cbullinger/copier-app-dest-1" "go-examples"
+            verify_dest_repo "cbullinger/copier-app-dest-2" "python-examples"
+            ;;
+        full)
+            check_app || exit 1
+            send_webhook "$PAYLOAD_FILE"
+            log_info "Waiting 10s for processing..."
+            sleep 10
+            verify_dest_repo "cbullinger/copier-app-dest-1" "go-examples"
+            verify_dest_repo "cbullinger/copier-app-dest-2" "python-examples"
+            ;;
+        *)
+            echo "Usage: $0 [webhook|verify|full]"
+            echo "  webhook - Send test webhook to app (default)"
+            echo "  verify  - Check destination repos for expected files"
+            echo "  full    - Send webhook and verify results"
+            exit 1
+            ;;
+    esac
+}
+
+main "$@"
+
diff --git a/scripts/test-and-check.sh b/scripts/test-and-check.sh
index cff02a3..2cf2508 100755
--- a/scripts/test-and-check.sh
+++ b/scripts/test-and-check.sh
@@ -15,7 +15,7 @@ echo -e "${BLUE}Testing webhook with example payload...${NC}"
 echo ""
 
 # Send webhook
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 
 echo ""
 echo -e "${GREEN}Webhook sent! Waiting 2 seconds for processing...${NC}"
diff --git a/service.yaml.example b/service.yaml.example
deleted file mode 100644
index e757792..0000000
--- a/service.yaml.example
+++ /dev/null
@@ -1,136 +0,0 @@
-apiVersion: serving.knative.dev/v1
-kind: Service
-metadata:
-  annotations:
-    run.googleapis.com/build-enable-automatic-updates: 'false'
-    run.googleapis.com/build-id: b757980d-a5c4-4c4e-8080-e592075e3d98
-    run.googleapis.com/build-image-uri: us-central1-docker.pkg.dev/github-copy-code-examples/cloud-run-source-deploy/examples-copier
-    run.googleapis.com/build-name: projects/1054147886816/locations/us-central1/builds/b757980d-a5c4-4c4e-8080-e592075e3d98
-    run.googleapis.com/build-source-location: gs://run-sources-github-copy-code-examples-us-central1/services/examples-copier/1761840094.638811-19107807ada84a65915888b814b6e6dd.zip#1761840095211493
-    run.googleapis.com/client-name: gcloud
-    run.googleapis.com/client-version: 542.0.0
-    run.googleapis.com/ingress: all
-    run.googleapis.com/ingress-status: all
-    run.googleapis.com/operation-id: 5b7f8ffb-c7c1-42f7-a0c5-8ec5532bc0c4
-    run.googleapis.com/urls: '["https://examples-copier-1054147886816.us-central1.run.app","https://examples-copier-7c5nckqo6a-uc.a.run.app"]'
-    serving.knative.dev/creator: cory.bullinger@gcp.corp.mongodb.com
-    serving.knative.dev/lastModifier: cory.bullinger@gcp.corp.mongodb.com
-  creationTimestamp: '2025-10-06T18:32:15.311946Z'
-  generation: 24
-  labels:
-    cloud.googleapis.com/location: us-central1
-  name: examples-copier
-  namespace: '1054147886816'
-  resourceVersion: AAZCYmPd434
-  selfLink: /apis/serving.knative.dev/v1/namespaces/1054147886816/services/examples-copier
-  uid: c8854b49-365c-4168-a33a-f8a58682a348
-spec:
-  template:
-    metadata:
-      annotations:
-        autoscaling.knative.dev/maxScale: '10'
-        run.googleapis.com/client-name: gcloud
-        run.googleapis.com/client-version: 542.0.0
-        run.googleapis.com/startup-cpu-boost: 'true'
-      labels:
-        client.knative.dev/nonce: xoklrkvxac
-        run.googleapis.com/startupProbeType: Default
-    spec:
-      containerConcurrency: 80
-      containers:
-      - env:
-        - name: WEBHOOK_SECRET
-          valueFrom:
-            secretKeyRef:
-              key: latest
-              name: webhook-secret
-        - name: MONGO_URI
-          valueFrom:
-            secretKeyRef:
-              key: latest
-              name: mongo-uri
-        - name: ADMIN_TOKEN
-          valueFrom:
-            secretKeyRef:
-              key: latest
-              name: admin-token
-        - name: GITHUB_APP_ID
-          value: '1166559'
-        - name: INSTALLATION_ID
-          value: '62138132'
-        - name: REPO_OWNER
-          value: mongodb
-        - name: REPO_NAME
-          value: docs-sample-apps
-        - name: SRC_BRANCH
-          value: main
-        - name: GITHUB_APP_PRIVATE_KEY_SECRET_NAME
-          value: projects/1054147886816/secrets/CODE_COPIER_PEM/versions/latest
-        - name: WEBHOOK_SECRET_NAME
-          value: projects/1054147886816/secrets/webhook-secret/versions/latest
-        - name: MONGO_URI_SECRET_NAME
-          value: projects/1054147886816/secrets/mongo-uri/versions/latest
-        - name: WEBSERVER_PATH
-          value: /events
-        - name: CONFIG_FILE
-          value: copier-config.yaml
-        - name: DEPRECATION_FILE
-          value: deprecated_examples.json
-        - name: COMMITTER_NAME
-          value: GitHub Copier App
-        - name: COMMITTER_EMAIL
-          value: bot@mongodb.com
-        - name: GOOGLE_CLOUD_PROJECT_ID
-          value: github-copy-code-examples
-        - name: COPIER_LOG_NAME
-          value: code-copier-log
-        - name: LOG_LEVEL
-          value: debug
-        - name: COPIER_DEBUG
-          value: 'true'
-        - name: AUDIT_ENABLED
-          value: 'false'
-        - name: METRICS_ENABLED
-          value: 'true'
-        - name: DRY_RUN
-          value: 'false'
-        image: us-central1-docker.pkg.dev/github-copy-code-examples/cloud-run-source-deploy/examples-copier@sha256:d61a9184ff45bea59d3dceba098f99c0bbce2242898607dac65009b8f9f0eae7
-        ports:
-        - containerPort: 8080
-          name: http1
-        resources:
-          limits:
-            cpu: '1'
-            memory: 512Mi
-        startupProbe:
-          failureThreshold: 1
-          periodSeconds: 240
-          tcpSocket:
-            port: 8080
-          timeoutSeconds: 240
-      serviceAccountName: 1054147886816-compute@developer.gserviceaccount.com
-      timeoutSeconds: 300
-  traffic:
-  - latestRevision: true
-    percent: 100
-status:
-  address:
-    url: https://examples-copier-7c5nckqo6a-uc.a.run.app
-  conditions:
-  - lastTransitionTime: '2025-10-30T16:03:29.978238Z'
-    status: 'True'
-    type: Ready
-  - lastTransitionTime: '2025-10-30T16:03:25.908981Z'
-    status: 'True'
-    type: ConfigurationsReady
-  - lastTransitionTime: '2025-10-30T16:03:29.928929Z'
-    status: 'True'
-    type: RoutesReady
-  latestCreatedRevisionName: examples-copier-00024-h29
-  latestReadyRevisionName: examples-copier-00024-h29
-  observedGeneration: 24
-  traffic:
-  - latestRevision: true
-    percent: 100
-    revisionName: examples-copier-00024-h29
-  url: https://examples-copier-7c5nckqo6a-uc.a.run.app
diff --git a/services/config_loader.go b/services/config_loader.go
index 32177b4..f3567dd 100644
--- a/services/config_loader.go
+++ b/services/config_loader.go
@@ -8,8 +8,8 @@ import (
 	"github.com/google/go-github/v48/github"
 	"gopkg.in/yaml.v3"
 
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
-	"github.com/mongodb/code-example-tooling/code-copier/types"
+	"github.com/grove-platform/github-copier/configs"
+	"github.com/grove-platform/github-copier/types"
 )
 
 // ConfigLoader handles loading and parsing configuration files
@@ -93,6 +93,9 @@ func retrieveConfigFileContent(ctx context.Context, filePath string, config *con
 	if err != nil {
 		return "", fmt.Errorf("failed to get config file: %w", err)
 	}
+	if fileContent == nil {
+		return "", fmt.Errorf("config file content is nil for path: %s", filePath)
+	}
 
 	// Decode content
 	content, err := fileContent.GetContent()
diff --git a/services/exclude_patterns_test.go b/services/exclude_patterns_test.go
index 6c9c49e..6bf5d49 100644
--- a/services/exclude_patterns_test.go
+++ b/services/exclude_patterns_test.go
@@ -3,7 +3,7 @@ package services
 import (
 	"testing"
 
-	"github.com/mongodb/code-example-tooling/code-copier/types"
+	"github.com/grove-platform/github-copier/types"
 )
 
 func TestExcludePatterns_PrefixPattern(t *testing.T) {
@@ -318,4 +318,3 @@ func TestExcludePatterns_ComplexScenarios(t *testing.T) {
 		})
 	}
 }
-
diff --git a/services/file_state_service.go b/services/file_state_service.go
index bdb72f2..cdbac21 100644
--- a/services/file_state_service.go
+++ b/services/file_state_service.go
@@ -3,15 +3,17 @@ package services
 import (
 	"sync"
 
-	"github.com/mongodb/code-example-tooling/code-copier/types"
+	"github.com/grove-platform/github-copier/types"
 )
 
 // FileStateService manages the state of files to upload and deprecate
 type FileStateService interface {
 	GetFilesToUpload() map[types.UploadKey]types.UploadFileContent
-	GetFilesToDeprecate() map[string]types.DeprecatedFileEntry
+	// GetFilesToDeprecate returns all deprecated file entries grouped by deprecation file name
+	GetFilesToDeprecate() map[string][]types.DeprecatedFileEntry
 	AddFileToUpload(key types.UploadKey, content types.UploadFileContent)
-	AddFileToDeprecate(file string, entry types.DeprecatedFileEntry)
+	// AddFileToDeprecate adds a file entry to the deprecation list for the given deprecation file
+	AddFileToDeprecate(deprecationFile string, entry types.DeprecatedFileEntry)
 	ClearFilesToUpload()
 	ClearFilesToDeprecate()
 }
@@ -20,14 +22,14 @@ type FileStateService interface {
 type DefaultFileStateService struct {
 	mu               sync.RWMutex
 	filesToUpload    map[types.UploadKey]types.UploadFileContent
-	filesToDeprecate map[string]types.DeprecatedFileEntry
+	filesToDeprecate map[string][]types.DeprecatedFileEntry // Changed: now stores slice of entries per file
 }
 
 // NewFileStateService creates a new file state service
 func NewFileStateService() FileStateService {
 	return &DefaultFileStateService{
 		filesToUpload:    make(map[types.UploadKey]types.UploadFileContent),
-		filesToDeprecate: make(map[string]types.DeprecatedFileEntry),
+		filesToDeprecate: make(map[string][]types.DeprecatedFileEntry),
 	}
 }
 
@@ -35,7 +37,7 @@ func NewFileStateService() FileStateService {
 func (fss *DefaultFileStateService) GetFilesToUpload() map[types.UploadKey]types.UploadFileContent {
 	fss.mu.RLock()
 	defer fss.mu.RUnlock()
-	
+
 	// Return a copy to prevent external modification
 	result := make(map[types.UploadKey]types.UploadFileContent, len(fss.filesToUpload))
 	for k, v := range fss.filesToUpload {
@@ -45,14 +47,18 @@ func (fss *DefaultFileStateService) GetFilesToUpload() map[types.UploadKey]types
 }
 
 // GetFilesToDeprecate returns a copy of the files to deprecate map
-func (fss *DefaultFileStateService) GetFilesToDeprecate() map[string]types.DeprecatedFileEntry {
+// The map key is the deprecation file name, and the value is a slice of all entries for that file
+func (fss *DefaultFileStateService) GetFilesToDeprecate() map[string][]types.DeprecatedFileEntry {
 	fss.mu.RLock()
 	defer fss.mu.RUnlock()
 
-	// Return a copy to prevent external modification
-	result := make(map[string]types.DeprecatedFileEntry, len(fss.filesToDeprecate))
+	// Return a deep copy to prevent external modification
+	result := make(map[string][]types.DeprecatedFileEntry, len(fss.filesToDeprecate))
 	for k, v := range fss.filesToDeprecate {
-		result[k] = v
+		// Copy the slice
+		entriesCopy := make([]types.DeprecatedFileEntry, len(v))
+		copy(entriesCopy, v)
+		result[k] = entriesCopy
 	}
 	return result
 }
@@ -65,19 +71,20 @@ func (fss *DefaultFileStateService) AddFileToUpload(key types.UploadKey, content
 	fss.filesToUpload[key] = content
 }
 
-// AddFileToDeprecate adds a file to the deprecation list
-func (fss *DefaultFileStateService) AddFileToDeprecate(file string, entry types.DeprecatedFileEntry) {
+// AddFileToDeprecate appends a file entry to the deprecation list for the given deprecation file
+// Multiple entries can be added for the same deprecation file
+func (fss *DefaultFileStateService) AddFileToDeprecate(deprecationFile string, entry types.DeprecatedFileEntry) {
 	fss.mu.Lock()
 	defer fss.mu.Unlock()
 
-	fss.filesToDeprecate[file] = entry
+	fss.filesToDeprecate[deprecationFile] = append(fss.filesToDeprecate[deprecationFile], entry)
 }
 
 // ClearFilesToUpload clears the files to upload map
 func (fss *DefaultFileStateService) ClearFilesToUpload() {
 	fss.mu.Lock()
 	defer fss.mu.Unlock()
-	
+
 	fss.filesToUpload = make(map[types.UploadKey]types.UploadFileContent)
 }
 
@@ -86,6 +93,5 @@ func (fss *DefaultFileStateService) ClearFilesToDeprecate() {
 	fss.mu.Lock()
 	defer fss.mu.Unlock()
 
-	fss.filesToDeprecate = make(map[string]types.DeprecatedFileEntry)
+	fss.filesToDeprecate = make(map[string][]types.DeprecatedFileEntry)
 }
-
diff --git a/services/file_state_service_test.go b/services/file_state_service_test.go
index 50cdb55..39bb2d9 100644
--- a/services/file_state_service_test.go
+++ b/services/file_state_service_test.go
@@ -5,8 +5,8 @@ import (
 	"testing"
 
 	"github.com/google/go-github/v48/github"
-	"github.com/mongodb/code-example-tooling/code-copier/services"
-	"github.com/mongodb/code-example-tooling/code-copier/types"
+	"github.com/grove-platform/github-copier/services"
+	"github.com/grove-platform/github-copier/types"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 )
@@ -61,11 +61,87 @@ func TestFileStateService_AddAndGetFilesToDeprecate(t *testing.T) {
 	files := service.GetFilesToDeprecate()
 	require.Len(t, files, 1)
 
-	retrieved, exists := files["deprecated.json"]
+	entries, exists := files["deprecated.json"]
 	require.True(t, exists)
-	assert.Equal(t, "old_example.go", retrieved.FileName)
-	assert.Equal(t, "org/repo", retrieved.Repo)
-	assert.Equal(t, "main", retrieved.Branch)
+	require.Len(t, entries, 1)
+	assert.Equal(t, "old_example.go", entries[0].FileName)
+	assert.Equal(t, "org/repo", entries[0].Repo)
+	assert.Equal(t, "main", entries[0].Branch)
+}
+
+func TestFileStateService_MultipleDeprecatedFilesAccumulate(t *testing.T) {
+	service := services.NewFileStateService()
+
+	// Add multiple files to the same deprecation file
+	entry1 := types.DeprecatedFileEntry{
+		FileName: "file1.go",
+		Repo:     "org/repo",
+		Branch:   "main",
+	}
+	entry2 := types.DeprecatedFileEntry{
+		FileName: "file2.go",
+		Repo:     "org/repo",
+		Branch:   "main",
+	}
+	entry3 := types.DeprecatedFileEntry{
+		FileName: "file3.go",
+		Repo:     "org/repo",
+		Branch:   "main",
+	}
+
+	service.AddFileToDeprecate("deprecated.json", entry1)
+	service.AddFileToDeprecate("deprecated.json", entry2)
+	service.AddFileToDeprecate("deprecated.json", entry3)
+
+	// Get files - should have all 3 entries
+	files := service.GetFilesToDeprecate()
+	require.Len(t, files, 1) // One deprecation file
+
+	entries, exists := files["deprecated.json"]
+	require.True(t, exists)
+	require.Len(t, entries, 3) // Three entries accumulated
+
+	// Verify all entries are present
+	fileNames := make([]string, len(entries))
+	for i, e := range entries {
+		fileNames[i] = e.FileName
+	}
+	assert.Contains(t, fileNames, "file1.go")
+	assert.Contains(t, fileNames, "file2.go")
+	assert.Contains(t, fileNames, "file3.go")
+}
+
+func TestFileStateService_MultipleDeprecationFiles(t *testing.T) {
+	service := services.NewFileStateService()
+
+	// Add entries to different deprecation files
+	entry1 := types.DeprecatedFileEntry{
+		FileName: "file1.go",
+		Repo:     "org/repo1",
+		Branch:   "main",
+	}
+	entry2 := types.DeprecatedFileEntry{
+		FileName: "file2.go",
+		Repo:     "org/repo2",
+		Branch:   "develop",
+	}
+
+	service.AddFileToDeprecate("deprecated_repo1.json", entry1)
+	service.AddFileToDeprecate("deprecated_repo2.json", entry2)
+
+	// Get files - should have 2 deprecation files
+	files := service.GetFilesToDeprecate()
+	require.Len(t, files, 2)
+
+	entries1, exists := files["deprecated_repo1.json"]
+	require.True(t, exists)
+	require.Len(t, entries1, 1)
+	assert.Equal(t, "file1.go", entries1[0].FileName)
+
+	entries2, exists := files["deprecated_repo2.json"]
+	require.True(t, exists)
+	require.Len(t, entries2, 1)
+	assert.Equal(t, "file2.go", entries2[0].FileName)
 }
 
 func TestFileStateService_ClearFilesToUpload(t *testing.T) {
@@ -301,4 +377,3 @@ func TestFileStateService_CommitStrategyTypes(t *testing.T) {
 		})
 	}
 }
-
diff --git a/services/github_auth.go b/services/github_auth.go
index 6e2f57a..683463f 100644
--- a/services/github_auth.go
+++ b/services/github_auth.go
@@ -7,7 +7,6 @@ import (
 	"encoding/json"
 	"fmt"
 	"io"
-	"log"
 	"net/http"
 	"os"
 	"time"
@@ -16,8 +15,7 @@ import (
 	"cloud.google.com/go/secretmanager/apiv1/secretmanagerpb"
 	"github.com/golang-jwt/jwt/v5"
 	"github.com/google/go-github/v48/github"
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
-	"github.com/pkg/errors"
+	"github.com/grove-platform/github-copier/configs"
 	"github.com/shurcooL/graphql"
 	"golang.org/x/oauth2"
 )
@@ -40,32 +38,36 @@ var jwtExpiry time.Time
 // ConfigurePermissions sets up the necessary permissions to interact with the GitHub API.
 // It retrieves the GitHub App's private key from Google Secret Manager, generates a JWT,
 // and exchanges it for an installation access token.
-func ConfigurePermissions() {
+func ConfigurePermissions() error {
 	envFilePath := os.Getenv("ENV_FILE")
 
 	_, err := configs.LoadEnvironment(envFilePath)
 	if err != nil {
-		log.Fatal(errors.Wrap(err, "Failed to load environment"))
+		return fmt.Errorf("failed to load environment: %w", err)
+	}
 
+	pemKey, err := getPrivateKeyFromSecret()
+	if err != nil {
+		return fmt.Errorf("failed to get private key: %w", err)
 	}
 
-	pemKey := getPrivateKeyFromSecret()
 	privateKey, err := jwt.ParseRSAPrivateKeyFromPEM(pemKey)
 	if err != nil {
-		log.Fatal(errors.Wrap(err, "Unable to parse RSA private key"))
+		return fmt.Errorf("unable to parse RSA private key: %w", err)
 	}
 
 	// Generate JWT — use the numeric GitHub App ID (GITHUB_APP_ID) as "iss"
 	token, err := generateGitHubJWT(os.Getenv(configs.AppId), privateKey)
 	if err != nil {
-		log.Fatal(errors.Wrap(err, "Error generating JWT"))
+		return fmt.Errorf("error generating JWT: %w", err)
 	}
 
 	installationToken, err := getInstallationAccessToken("", token, HTTPClient)
 	if err != nil {
-		log.Fatal(errors.Wrap(err, "Error getting installation access token"))
+		return fmt.Errorf("error getting installation access token: %w", err)
 	}
 	InstallationAccessToken = installationToken
+	return nil
 }
 
 // generateGitHubJWT creates a JWT for GitHub App authentication.
@@ -88,25 +90,25 @@ func generateGitHubJWT(appID string, privateKey *rsa.PrivateKey) (string, error)
 
 // getPrivateKeyFromSecret retrieves the GitHub App's private key from Google Secret Manager.
 // It supports local testing by allowing the key to be provided via environment variables.
-func getPrivateKeyFromSecret() []byte {
+func getPrivateKeyFromSecret() ([]byte, error) {
 	if os.Getenv("SKIP_SECRET_MANAGER") == "true" { // for tests and local runs
 		if pem := os.Getenv("GITHUB_APP_PRIVATE_KEY"); pem != "" {
-			return []byte(pem)
+			return []byte(pem), nil
 		}
 		if b64 := os.Getenv("GITHUB_APP_PRIVATE_KEY_B64"); b64 != "" {
 			dec, err := base64.StdEncoding.DecodeString(b64)
 			if err != nil {
-				log.Fatalf("Invalid base64 private key: %v", err)
+				return nil, fmt.Errorf("invalid base64 private key: %w", err)
 			}
-			return dec
+			return dec, nil
 		}
-		log.Fatalf("SKIP_SECRET_MANAGER=true but no GITHUB_APP_PRIVATE_KEY or GITHUB_APP_PRIVATE_KEY_B64 set")
+		return nil, fmt.Errorf("SKIP_SECRET_MANAGER=true but no GITHUB_APP_PRIVATE_KEY or GITHUB_APP_PRIVATE_KEY_B64 set")
 	}
 	ctx := context.Background()
 	client, err := secretmanager.NewClient(ctx)
 
 	if err != nil {
-		log.Fatalf("Failed to create Secret Manager client: %v", err)
+		return nil, fmt.Errorf("failed to create Secret Manager client: %w", err)
 	}
 	defer client.Close()
 
@@ -120,9 +122,9 @@ func getPrivateKeyFromSecret() []byte {
 	}
 	result, err := client.AccessSecretVersion(ctx, req)
 	if err != nil {
-		log.Fatalf("Failed to access secret version: %v", err)
+		return nil, fmt.Errorf("failed to access secret version: %w", err)
 	}
-	return result.Payload.Data
+	return result.Payload.Data, nil
 }
 
 // getWebhookSecretFromSecretManager retrieves the webhook secret from Google Cloud Secret Manager
@@ -273,14 +275,16 @@ func GetRestClient() *github.Client {
 	return github.NewClient(httpClient)
 }
 
-func GetGraphQLClient() *graphql.Client {
+func GetGraphQLClient() (*graphql.Client, error) {
 	if InstallationAccessToken == "" {
-		ConfigurePermissions()
+		if err := ConfigurePermissions(); err != nil {
+			return nil, fmt.Errorf("failed to configure permissions: %w", err)
+		}
 	}
 	client := graphql.NewClient("https://api.github.com/graphql", &http.Client{
 		Transport: &transport{token: InstallationAccessToken},
 	})
-	return client
+	return client, nil
 }
 
 // getOrRefreshJWT returns a valid JWT token, generating a new one if expired
@@ -291,7 +295,11 @@ func getOrRefreshJWT() (string, error) {
 	}
 
 	// Generate new JWT
-	pemKey := getPrivateKeyFromSecret()
+	pemKey, err := getPrivateKeyFromSecret()
+	if err != nil {
+		return "", fmt.Errorf("failed to get private key: %w", err)
+	}
+
 	privateKey, err := jwt.ParseRSAPrivateKeyFromPEM(pemKey)
 	if err != nil {
 		return "", fmt.Errorf("unable to parse RSA private key: %w", err)
diff --git a/services/github_auth_test.go b/services/github_auth_test.go
index d922869..cbb6f6c 100644
--- a/services/github_auth_test.go
+++ b/services/github_auth_test.go
@@ -5,7 +5,7 @@ import (
 	"testing"
 	"time"
 
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
+	"github.com/grove-platform/github-copier/configs"
 )
 
 func TestGenerateGitHubJWT_EmptyAppID(t *testing.T) {
diff --git a/services/github_read.go b/services/github_read.go
index fa6be3b..e213712 100644
--- a/services/github_read.go
+++ b/services/github_read.go
@@ -7,8 +7,8 @@ import (
 	"os"
 
 	"github.com/google/go-github/v48/github"
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
-	. "github.com/mongodb/code-example-tooling/code-copier/types"
+	"github.com/grove-platform/github-copier/configs"
+	. "github.com/grove-platform/github-copier/types"
 	"github.com/shurcooL/githubv4"
 )
 
@@ -21,10 +21,15 @@ import (
 func GetFilesChangedInPr(owner string, repo string, pr_number int) ([]ChangedFile, error) {
 	if InstallationAccessToken == "" {
 		log.Println("No installation token provided")
-		ConfigurePermissions()
+		if err := ConfigurePermissions(); err != nil {
+			return nil, fmt.Errorf("failed to configure permissions: %w", err)
+		}
 	}
 
-	client := GetGraphQLClient()
+	client, err := GetGraphQLClient()
+	if err != nil {
+		return nil, fmt.Errorf("failed to get GraphQL client: %w", err)
+	}
 	ctx := context.Background()
 
 	var changedFiles []ChangedFile
@@ -106,7 +111,10 @@ func RetrieveFileContents(filePath string) (github.RepositoryContent, error) {
 			})
 
 	if err != nil {
-		LogCritical(fmt.Sprintf("Error getting file content: %v", err))
+		return github.RepositoryContent{}, fmt.Errorf("failed to get file content for %s: %w", filePath, err)
+	}
+	if fileContent == nil {
+		return github.RepositoryContent{}, fmt.Errorf("file content is nil for path: %s", filePath)
 	}
 	return *fileContent, nil
 }
diff --git a/services/github_read_test.go b/services/github_read_test.go
index 5bc0bcc..3f79a59 100644
--- a/services/github_read_test.go
+++ b/services/github_read_test.go
@@ -5,10 +5,10 @@ import (
 	"testing"
 
 	"github.com/google/go-github/v48/github"
-	"github.com/mongodb/code-example-tooling/code-copier/services"
+	"github.com/grove-platform/github-copier/services"
 	"github.com/stretchr/testify/require"
 
-	test "github.com/mongodb/code-example-tooling/code-copier/tests"
+	test "github.com/grove-platform/github-copier/tests"
 )
 
 // Helper to b64-encode inline strings
diff --git a/services/github_write_to_source.go b/services/github_write_to_source.go
index 237d378..c1941cd 100644
--- a/services/github_write_to_source.go
+++ b/services/github_write_to_source.go
@@ -8,8 +8,8 @@ import (
 	"time"
 
 	"github.com/google/go-github/v48/github"
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
-	. "github.com/mongodb/code-example-tooling/code-copier/types"
+	"github.com/grove-platform/github-copier/configs"
+	. "github.com/grove-platform/github-copier/types"
 )
 
 func UpdateDeprecationFile() {
@@ -36,6 +36,10 @@ func UpdateDeprecationFile() {
 		LogError(fmt.Sprintf("Error getting deprecation file: %v", err))
 		return
 	}
+	if fileContent == nil {
+		LogError("Deprecation file content is nil")
+		return
+	}
 
 	content, err := fileContent.GetContent()
 	if err != nil {
@@ -80,6 +84,11 @@ func uploadDeprecationFileChanges(message string, newDeprecationFileContents str
 
 	if err != nil {
 		LogError(fmt.Sprintf("Error getting deprecation file contents: %v", err))
+		return
+	}
+	if targetFileContent == nil {
+		LogError("Target deprecation file content is nil")
+		return
 	}
 
 	options := &github.RepositoryContentFileOptions{
@@ -96,5 +105,5 @@ func uploadDeprecationFileChanges(message string, newDeprecationFileContents str
 		LogError(fmt.Sprintf("Cannot update deprecation file: %v", err))
 	}
 
-	LogInfo(fmt.Sprintf("Deprecation file updated."))
+	LogInfo("Deprecation file updated.")
 }
diff --git a/services/github_write_to_source_test.go b/services/github_write_to_source_test.go
index d98c88a..c9af808 100644
--- a/services/github_write_to_source_test.go
+++ b/services/github_write_to_source_test.go
@@ -3,7 +3,7 @@ package services
 import (
 	"testing"
 
-	. "github.com/mongodb/code-example-tooling/code-copier/types"
+	. "github.com/grove-platform/github-copier/types"
 )
 
 func TestUpdateDeprecationFile_EmptyList(t *testing.T) {
diff --git a/services/github_write_to_target.go b/services/github_write_to_target.go
index 8d0eedb..e77066e 100644
--- a/services/github_write_to_target.go
+++ b/services/github_write_to_target.go
@@ -3,15 +3,14 @@ package services
 import (
 	"context"
 	"fmt"
-	"log"
 	"net/http"
 	"os"
 	"strings"
 	"time"
 
 	"github.com/google/go-github/v48/github"
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
-	. "github.com/mongodb/code-example-tooling/code-copier/types"
+	"github.com/grove-platform/github-copier/configs"
+	. "github.com/grove-platform/github-copier/types"
 	"github.com/pkg/errors"
 )
 
@@ -22,8 +21,6 @@ import (
 var FilesToUpload map[UploadKey]UploadFileContent
 var FilesToDeprecate map[string]Configs
 
-
-
 // repoOwner returns the config repository owner from environment variables.
 func repoOwner() string { return os.Getenv(configs.ConfigRepoOwner) }
 
@@ -241,7 +238,10 @@ func addFilesViaPR(ctx context.Context, client *github.Client, key UploadKey,
 		if err = mergePR(ctx, client, key.RepoName, pr.GetNumber()); err != nil {
 			return fmt.Errorf("merge PR: %w", err)
 		}
-		deleteBranchIfExists(ctx, client, key.RepoName, &github.Reference{Ref: github.String("refs/heads/" + tempBranch)})
+		if err = deleteBranchIfExists(ctx, client, key.RepoName, &github.Reference{Ref: github.String("refs/heads/" + tempBranch)}); err != nil {
+			// Log but don't fail - branch cleanup is not critical
+			LogWarning(fmt.Sprintf("Failed to delete temp branch after merge: %v", err))
+		}
 	} else {
 		LogInfo(fmt.Sprintf("PR created and awaiting review: #%d", pr.GetNumber()))
 	}
@@ -289,8 +289,10 @@ func createBranch(ctx context.Context, client *github.Client, repo, newBranch st
 	}
 
 	// *** Check if branch (newBranchRef) already exists and delete it ***
-	newBranchRef, _, err := client.Git.GetRef(ctx, owner, repoName, fmt.Sprintf("%s%s", "refs/heads/", newBranch))
-	deleteBranchIfExists(ctx, client, normalizedRepo, newBranchRef)
+	newBranchRef, _, _ := client.Git.GetRef(ctx, owner, repoName, fmt.Sprintf("%s%s", "refs/heads/", newBranch))
+	if err := deleteBranchIfExists(ctx, client, normalizedRepo, newBranchRef); err != nil {
+		return nil, fmt.Errorf("failed to delete existing branch %s: %w", newBranch, err)
+	}
 
 	newRef := &github.Reference{
 		Ref: github.String(fmt.Sprintf("%s%s", "refs/heads/", newBranch)),
@@ -441,10 +443,11 @@ func mergePR(ctx context.Context, client *github.Client, repo string, pr_number
 }
 
 // deleteBranchIfExists deletes the specified branch if it exists, except for 'main'.
-func deleteBranchIfExists(backgroundContext context.Context, client *github.Client, repo string, ref *github.Reference) {
+// Returns an error if attempting to delete the main branch or if deletion fails.
+func deleteBranchIfExists(backgroundContext context.Context, client *github.Client, repo string, ref *github.Reference) error {
 	// Early return if ref is nil (branch doesn't exist)
 	if ref == nil {
-		return
+		return nil
 	}
 
 	// Normalize repo name for consistent logging
@@ -453,7 +456,7 @@ func deleteBranchIfExists(backgroundContext context.Context, client *github.Clie
 
 	if ref.GetRef() == "refs/heads/main" {
 		LogError("I refuse to delete branch 'main'.")
-		log.Fatal()
+		return fmt.Errorf("refusing to delete protected branch 'main'")
 	}
 
 	LogInfo(fmt.Sprintf("Deleting branch %s on %s", ref.GetRef(), normalizedRepo))
@@ -463,13 +466,15 @@ func deleteBranchIfExists(backgroundContext context.Context, client *github.Clie
 		_, err = client.Git.DeleteRef(backgroundContext, owner, repoName, ref.GetRef())
 		if err != nil {
 			LogCritical(fmt.Sprintf("Error deleting branch: %v\n", err))
+			return fmt.Errorf("failed to delete branch %s: %w", ref.GetRef(), err)
 		}
 	}
+	return nil
 }
 
 // DeleteBranchIfExistsExported is an exported wrapper for testing deleteBranchIfExists
-func DeleteBranchIfExistsExported(ctx context.Context, client *github.Client, repo string, ref *github.Reference) {
-	deleteBranchIfExists(ctx, client, repo, ref)
+func DeleteBranchIfExistsExported(ctx context.Context, client *github.Client, repo string, ref *github.Reference) error {
+	return deleteBranchIfExists(ctx, client, repo, ref)
 }
 
 // parseIntWithDefault parses a string to int, returning defaultValue on error
diff --git a/services/github_write_to_target_test.go b/services/github_write_to_target_test.go
index be93035..a645836 100644
--- a/services/github_write_to_target_test.go
+++ b/services/github_write_to_target_test.go
@@ -15,14 +15,14 @@ import (
 	"testing"
 
 	"github.com/google/go-github/v48/github"
+	"github.com/grove-platform/github-copier/configs"
+	"github.com/grove-platform/github-copier/services"
+	"github.com/grove-platform/github-copier/types"
 	"github.com/jarcoal/httpmock"
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
-	"github.com/mongodb/code-example-tooling/code-copier/services"
-	"github.com/mongodb/code-example-tooling/code-copier/types"
 	"github.com/stretchr/testify/require"
 
 	// test helpers (utils.go)
-	test "github.com/mongodb/code-example-tooling/code-copier/tests"
+	test "github.com/grove-platform/github-copier/tests"
 )
 
 func TestMain(m *testing.M) {
@@ -280,7 +280,8 @@ func TestAddFilesToTargetRepoBranch_ViaPR_Succeeds(t *testing.T) {
 	// Force fresh token; stub token endpoint then configure permissions.
 	services.InstallationAccessToken = ""
 	test.MockGitHubAppTokenEndpoint(os.Getenv(configs.InstallationId))
-	services.ConfigurePermissions()
+	err := services.ConfigurePermissions()
+	require.NoError(t, err, "ConfigurePermissions should succeed")
 
 	// Set up cached token for the org to bypass GitHub App auth
 	test.SetupOrgToken(owner, "test-token")
@@ -389,8 +390,6 @@ func TestAddFilesToTargetRepoBranch_ViaPR_Succeeds(t *testing.T) {
 	services.FilesToUpload = nil
 }
 
-
-
 // --- Added critical tests for merge conflicts and configuration/default priorities ---
 
 func TestAddFiles_DirectConflict_NonFastForward(t *testing.T) {
@@ -445,7 +444,8 @@ func TestAddFiles_ViaPR_MergeConflict_Dirty_NotMerged(t *testing.T) {
 	// Fresh token path
 	services.InstallationAccessToken = ""
 	test.MockGitHubAppTokenEndpoint(os.Getenv(configs.InstallationId))
-	services.ConfigurePermissions()
+	err := services.ConfigurePermissions()
+	require.NoError(t, err, "ConfigurePermissions should succeed")
 
 	// Set up cached token for the org to bypass GitHub App auth
 	test.SetupOrgToken(owner, "test-token")
@@ -467,6 +467,11 @@ func TestAddFiles_ViaPR_MergeConflict_Dirty_NotMerged(t *testing.T) {
 			"ref": "refs/heads/copier/20250101-000000", "object": map[string]any{"sha": "baseSha"},
 		}),
 	)
+	// Mock DELETE for existing temp branch cleanup
+	httpmock.RegisterRegexpResponder("DELETE",
+		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+repo+`/git/refs/heads/`+tempHead+`$`),
+		httpmock.NewStringResponder(204, ""),
+	)
 	httpmock.RegisterRegexpResponder("POST",
 		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+repo+`/git/trees(\?.*)?$`),
 		httpmock.NewJsonResponderOrPanic(201, map[string]any{"sha": "newTreeSha"}),
@@ -484,7 +489,7 @@ func TestAddFiles_ViaPR_MergeConflict_Dirty_NotMerged(t *testing.T) {
 	pr_number := 77
 	httpmock.RegisterResponder("POST",
 		"https://api.github.com/repos/"+owner+"/"+repo+"/pulls",
-		httpmock.NewJsonResponderOrPanic(201, map[string]any{"number": pr_number, "html_url": "https://github.com/"+owner+"/"+repo+"/pull/77"}),
+		httpmock.NewJsonResponderOrPanic(201, map[string]any{"number": pr_number, "html_url": "https://github.com/" + owner + "/" + repo + "/pull/77"}),
 	)
 	// PR mergeability check returns dirty -> not mergeable
 	httpmock.RegisterResponder("GET",
@@ -513,13 +518,14 @@ func TestAddFiles_ViaPR_MergeConflict_Dirty_NotMerged(t *testing.T) {
 	// Assertions
 	info := httpmock.GetCallCountInfo()
 	require.Equal(t, 1, info["POST "+createRefURL])
- require.Equal(t, 1, test.CountByMethodAndURLRegexp("POST",
+	require.Equal(t, 1, test.CountByMethodAndURLRegexp("POST",
 		regexp.MustCompile(`/repos/`+regexp.QuoteMeta(owner)+`/`+regexp.QuoteMeta(repo)+`/pulls$`)))
 	// No merge call should have been made
- require.Equal(t, 0, test.CountByMethodAndURLRegexp("PUT",
+	require.Equal(t, 0, test.CountByMethodAndURLRegexp("PUT",
 		regexp.MustCompile(`/repos/`+regexp.QuoteMeta(owner)+`/`+regexp.QuoteMeta(repo)+`/pulls/77/merge$`)))
-	// No delete of temp ref because we returned early
- require.Equal(t, 0, test.CountByMethodAndURLRegexp("DELETE",
+	// Only 1 DELETE call for initial cleanup of existing branch (before creating new one)
+	// No additional DELETE after merge conflict because we returned early
+	require.Equal(t, 1, test.CountByMethodAndURLRegexp("DELETE",
 		regexp.MustCompile(`/repos/`+regexp.QuoteMeta(owner)+`/`+regexp.QuoteMeta(repo)+`/git/refs/heads/copier/\d{8}-\d{6}$`)))
 
 	services.FilesToUpload = nil
@@ -593,7 +599,8 @@ func TestPriority_PRTitleDefaultsToCommitMessage_And_NoAutoMergeWhenConfigPresen
 	// Token setup
 	services.InstallationAccessToken = ""
 	test.MockGitHubAppTokenEndpoint(os.Getenv(configs.InstallationId))
-	services.ConfigurePermissions()
+	err := services.ConfigurePermissions()
+	require.NoError(t, err, "ConfigurePermissions should succeed")
 
 	// Set up cached token for the org to bypass GitHub App auth
 	test.SetupOrgToken(owner, "test-token")
@@ -604,11 +611,16 @@ func TestPriority_PRTitleDefaultsToCommitMessage_And_NoAutoMergeWhenConfigPresen
 		httpmock.NewJsonResponderOrPanic(200, map[string]any{"ref": "refs/heads/" + baseBranch, "object": map[string]any{"sha": "baseSha"}}),
 	)
 	_ = test.MockCreateRef(owner, repo)
-		tempHead := `copier/\d{8}-\d{6}`
+	tempHead := `copier/\d{8}-\d{6}`
 	httpmock.RegisterRegexpResponder("GET",
 		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+repo+`/git/ref/(?:refs/)?heads/`+tempHead+`$`),
 		httpmock.NewJsonResponderOrPanic(200, map[string]any{"ref": "refs/heads/copier/20250101-000000", "object": map[string]any{"sha": "baseSha"}}),
 	)
+	// Mock DELETE for existing temp branch cleanup
+	httpmock.RegisterRegexpResponder("DELETE",
+		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+repo+`/git/refs/heads/`+tempHead+`$`),
+		httpmock.NewStringResponder(204, ""),
+	)
 	httpmock.RegisterRegexpResponder("POST",
 		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+repo+`/git/trees(\?.*)?$`),
 		httpmock.NewJsonResponderOrPanic(201, map[string]any{"sha": "t"}),
@@ -666,7 +678,8 @@ func TestDeleteBranchIfExists_NilReference(t *testing.T) {
 	// Force fresh token
 	services.InstallationAccessToken = ""
 	test.MockGitHubAppTokenEndpoint(os.Getenv(configs.InstallationId))
-	services.ConfigurePermissions()
+	err := services.ConfigurePermissions()
+	require.NoError(t, err, "ConfigurePermissions should succeed")
 
 	// This should not panic or make any API calls when ref is nil
 	// We're testing that the function returns early without attempting to delete
@@ -674,7 +687,8 @@ func TestDeleteBranchIfExists_NilReference(t *testing.T) {
 	client := services.GetRestClient()
 
 	// Call with nil reference - should return immediately without error
-	services.DeleteBranchIfExistsExported(ctx, client, "test-org/test-repo", nil)
+	err = services.DeleteBranchIfExistsExported(ctx, client, "test-org/test-repo", nil)
+	require.NoError(t, err, "DeleteBranchIfExistsExported should succeed with nil ref")
 
 	// Verify no DELETE requests were made (since ref was nil)
 	require.Equal(t, 0, test.CountByMethodAndURLRegexp("DELETE", regexp.MustCompile(`/git/refs/`)))
diff --git a/services/health_metrics.go b/services/health_metrics.go
index 9e48e97..104e4d2 100644
--- a/services/health_metrics.go
+++ b/services/health_metrics.go
@@ -9,18 +9,18 @@ import (
 
 // HealthStatus represents the health status of the application
 type HealthStatus struct {
-	Status              string                 `json:"status"`
-	Started             bool                   `json:"started"`
-	GitHub              GitHubHealthStatus     `json:"github"`
-	Queues              QueueHealthStatus      `json:"queues"`
-	AuditLogger         AuditLoggerHealthStatus `json:"audit_logger,omitempty"`
-	Uptime              string                 `json:"uptime"`
+	Status      string                  `json:"status"`
+	Started     bool                    `json:"started"`
+	GitHub      GitHubHealthStatus      `json:"github"`
+	Queues      QueueHealthStatus       `json:"queues"`
+	AuditLogger AuditLoggerHealthStatus `json:"audit_logger,omitempty"`
+	Uptime      string                  `json:"uptime"`
 }
 
 // GitHubHealthStatus represents GitHub API health
 type GitHubHealthStatus struct {
-	Status       string `json:"status"`
-	Authenticated bool  `json:"authenticated"`
+	Status        string `json:"status"`
+	Authenticated bool   `json:"authenticated"`
 }
 
 // QueueHealthStatus represents queue health
@@ -37,40 +37,40 @@ type AuditLoggerHealthStatus struct {
 
 // MetricsData represents application metrics
 type MetricsData struct {
-	Webhooks   WebhookMetrics   `json:"webhooks"`
-	Files      FileMetrics      `json:"files"`
-	GitHubAPI  GitHubAPIMetrics `json:"github_api"`
-	Queues     QueueMetrics     `json:"queues"`
-	System     SystemMetrics    `json:"system"`
+	Webhooks  WebhookMetrics   `json:"webhooks"`
+	Files     FileMetrics      `json:"files"`
+	GitHubAPI GitHubAPIMetrics `json:"github_api"`
+	Queues    QueueMetrics     `json:"queues"`
+	System    SystemMetrics    `json:"system"`
 }
 
 // WebhookMetrics represents webhook processing metrics
 type WebhookMetrics struct {
-	Received       int64              `json:"received"`
-	Processed      int64              `json:"processed"`
-	Failed         int64              `json:"failed"`
-	Ignored        int64              `json:"ignored"` // Non-PR events
-	EventTypes     map[string]int64   `json:"event_types"` // Count by event type
-	SuccessRate    float64            `json:"success_rate"`
+	Received       int64               `json:"received"`
+	Processed      int64               `json:"processed"`
+	Failed         int64               `json:"failed"`
+	Ignored        int64               `json:"ignored"`     // Non-PR events
+	EventTypes     map[string]int64    `json:"event_types"` // Count by event type
+	SuccessRate    float64             `json:"success_rate"`
 	ProcessingTime ProcessingTimeStats `json:"processing_time"`
 }
 
 // FileMetrics represents file operation metrics
 type FileMetrics struct {
-	Matched          int64              `json:"matched"`
-	Uploaded         int64              `json:"uploaded"`
-	UploadFailed     int64              `json:"upload_failed"`
-	Deprecated       int64              `json:"deprecated"`
-	UploadSuccessRate float64           `json:"upload_success_rate"`
-	UploadTime       ProcessingTimeStats `json:"upload_time"`
+	Matched           int64               `json:"matched"`
+	Uploaded          int64               `json:"uploaded"`
+	UploadFailed      int64               `json:"upload_failed"`
+	Deprecated        int64               `json:"deprecated"`
+	UploadSuccessRate float64             `json:"upload_success_rate"`
+	UploadTime        ProcessingTimeStats `json:"upload_time"`
 }
 
 // GitHubAPIMetrics represents GitHub API usage metrics
 type GitHubAPIMetrics struct {
-	Calls      int64              `json:"calls"`
-	Errors     int64              `json:"errors"`
-	ErrorRate  float64            `json:"error_rate"`
-	RateLimit  RateLimitInfo      `json:"rate_limit"`
+	Calls     int64         `json:"calls"`
+	Errors    int64         `json:"errors"`
+	ErrorRate float64       `json:"error_rate"`
+	RateLimit RateLimitInfo `json:"rate_limit"`
 }
 
 // RateLimitInfo represents GitHub API rate limit info
@@ -103,21 +103,21 @@ type ProcessingTimeStats struct {
 
 // MetricsCollector collects and manages application metrics
 type MetricsCollector struct {
-	mu              sync.RWMutex
-	startTime       time.Time
-	webhookReceived int64
-	webhookProcessed int64
-	webhookFailed   int64
-	webhookIgnored  int64 // Non-PR events that were ignored
-	eventTypes      map[string]int64 // Count by event type
-	filesMatched    int64
-	filesUploaded   int64
+	mu                sync.RWMutex
+	startTime         time.Time
+	webhookReceived   int64
+	webhookProcessed  int64
+	webhookFailed     int64
+	webhookIgnored    int64            // Non-PR events that were ignored
+	eventTypes        map[string]int64 // Count by event type
+	filesMatched      int64
+	filesUploaded     int64
 	filesUploadFailed int64
-	filesDeprecated int64
-	githubAPICalls  int64
-	githubAPIErrors int64
-	processingTimes []time.Duration
-	uploadTimes     []time.Duration
+	filesDeprecated   int64
+	githubAPICalls    int64
+	githubAPIErrors   int64
+	processingTimes   []time.Duration
+	uploadTimes       []time.Duration
 }
 
 // NewMetricsCollector creates a new metrics collector
@@ -143,7 +143,7 @@ func (mc *MetricsCollector) RecordWebhookProcessed(duration time.Duration) {
 	defer mc.mu.Unlock()
 	mc.webhookProcessed++
 	mc.processingTimes = append(mc.processingTimes, duration)
-	
+
 	// Keep only last 1000 entries
 	if len(mc.processingTimes) > 1000 {
 		mc.processingTimes = mc.processingTimes[len(mc.processingTimes)-1000:]
@@ -178,7 +178,7 @@ func (mc *MetricsCollector) RecordFileUploaded(duration time.Duration) {
 	defer mc.mu.Unlock()
 	mc.filesUploaded++
 	mc.uploadTimes = append(mc.uploadTimes, duration)
-	
+
 	// Keep only last 1000 entries
 	if len(mc.uploadTimes) > 1000 {
 		mc.uploadTimes = mc.uploadTimes[len(mc.uploadTimes)-1000:]
@@ -276,12 +276,12 @@ func (mc *MetricsCollector) GetMetrics(fileStateService FileStateService) Metric
 			ProcessingTime: calculateStats(mc.processingTimes),
 		},
 		Files: FileMetrics{
-			Matched:          mc.filesMatched,
-			Uploaded:         mc.filesUploaded,
-			UploadFailed:     mc.filesUploadFailed,
-			Deprecated:       mc.filesDeprecated,
+			Matched:           mc.filesMatched,
+			Uploaded:          mc.filesUploaded,
+			UploadFailed:      mc.filesUploadFailed,
+			Deprecated:        mc.filesDeprecated,
 			UploadSuccessRate: uploadSuccessRate,
-			UploadTime:       calculateStats(mc.uploadTimes),
+			UploadTime:        calculateStats(mc.uploadTimes),
 		},
 		GitHubAPI: GitHubAPIMetrics{
 			Calls:     mc.githubAPICalls,
@@ -351,7 +351,7 @@ func HealthHandler(fileStateService FileStateService, startTime time.Time) http.
 			Status:  "healthy",
 			Started: true,
 			GitHub: GitHubHealthStatus{
-				Status:       "healthy",
+				Status:        "healthy",
 				Authenticated: true,
 			},
 			Queues: QueueHealthStatus{
@@ -362,7 +362,7 @@ func HealthHandler(fileStateService FileStateService, startTime time.Time) http.
 		}
 
 		w.Header().Set("Content-Type", "application/json")
-		json.NewEncoder(w).Encode(health)
+		_ = json.NewEncoder(w).Encode(health)
 	}
 }
 
@@ -371,7 +371,6 @@ func MetricsHandler(metricsCollector *MetricsCollector, fileStateService FileSta
 	return func(w http.ResponseWriter, r *http.Request) {
 		metrics := metricsCollector.GetMetrics(fileStateService)
 		w.Header().Set("Content-Type", "application/json")
-		json.NewEncoder(w).Encode(metrics)
+		_ = json.NewEncoder(w).Encode(metrics)
 	}
 }
-
diff --git a/services/health_metrics_test.go b/services/health_metrics_test.go
index 9a3dc9b..c3ede8d 100644
--- a/services/health_metrics_test.go
+++ b/services/health_metrics_test.go
@@ -7,8 +7,8 @@ import (
 	"testing"
 	"time"
 
-	"github.com/mongodb/code-example-tooling/code-copier/services"
-	"github.com/mongodb/code-example-tooling/code-copier/types"
+	"github.com/grove-platform/github-copier/services"
+	"github.com/grove-platform/github-copier/types"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 )
@@ -228,11 +228,11 @@ func TestMetricsCollector_ZeroValues(t *testing.T) {
 
 func TestMetricsCollector_SuccessRateCalculation(t *testing.T) {
 	tests := []struct {
-		name        string
-		received    int
-		processed   int
-		failed      int
-		wantRate    float64
+		name      string
+		received  int
+		processed int
+		failed    int
+		wantRate  float64
 	}{
 		{
 			name:      "all success",
@@ -319,4 +319,3 @@ func TestMetricsCollector_ConcurrentAccess(t *testing.T) {
 	metrics := collector.GetMetrics(fileStateService)
 	assert.Greater(t, metrics.Webhooks.Received, int64(0))
 }
-
diff --git a/services/logger.go b/services/logger.go
index 4d51c27..e6c13b5 100644
--- a/services/logger.go
+++ b/services/logger.go
@@ -11,9 +11,15 @@ import (
 	"time"
 
 	"cloud.google.com/go/logging"
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
+	"github.com/grove-platform/github-copier/configs"
 )
 
+// contextKey is a custom type for context keys to avoid collisions
+type contextKey string
+
+// requestIDKey is the context key for request IDs
+const requestIDKey contextKey = "request_id"
+
 var googleInfoLogger *log.Logger
 var googleWarningLogger *log.Logger
 var googleErrorLogger *log.Logger
@@ -121,7 +127,6 @@ func isCloudLoggingDisabled() bool {
 	return strings.EqualFold(os.Getenv("COPIER_DISABLE_CLOUD_LOGGING"), "true")
 }
 
-
 // Context-aware logging functions
 
 // LogInfoCtx logs an info message with context and additional fields
@@ -197,7 +202,7 @@ func LogAndReturnError(ctx context.Context, operation string, message string, er
 
 // formatLogMessage formats a log message with context and fields
 func formatLogMessage(ctx context.Context, message string, fields map[string]interface{}) string {
-	if fields == nil || len(fields) == 0 {
+	if len(fields) == 0 {
 		return message
 	}
 
@@ -215,8 +220,8 @@ func WithRequestID(r *http.Request) (context.Context, string) {
 	// Generate a simple request ID
 	requestID := fmt.Sprintf("%d", time.Now().UnixNano())
 
-	// Add to context
-	ctx := context.WithValue(r.Context(), "request_id", requestID)
+	// Add to context using typed key to avoid collisions
+	ctx := context.WithValue(r.Context(), requestIDKey, requestID)
 
 	return ctx, requestID
 }
diff --git a/services/logger_test.go b/services/logger_test.go
index a764673..19f148f 100644
--- a/services/logger_test.go
+++ b/services/logger_test.go
@@ -13,11 +13,11 @@ import (
 
 func TestLogDebug(t *testing.T) {
 	tests := []struct {
-		name          string
-		logLevel      string
-		copierDebug   string
-		message       string
-		shouldLog     bool
+		name        string
+		logLevel    string
+		copierDebug string
+		message     string
+		shouldLog   bool
 	}{
 		{
 			name:        "debug enabled via LOG_LEVEL",
@@ -289,15 +289,15 @@ func TestLogFileOperation(t *testing.T) {
 
 func TestWithRequestID(t *testing.T) {
 	req := httptest.NewRequest("GET", "/test", nil)
-	
+
 	ctx, requestID := WithRequestID(req)
-	
+
 	if requestID == "" {
 		t.Error("Expected non-empty request ID")
 	}
 
-	// Check that request ID is in context
-	ctxValue := ctx.Value("request_id")
+	// Check that request ID is in context using the typed key
+	ctxValue := ctx.Value(requestIDKey)
 	if ctxValue == nil {
 		t.Error("Expected request_id in context")
 	}
@@ -405,4 +405,3 @@ func TestIsCloudLoggingDisabled(t *testing.T) {
 		})
 	}
 }
-
diff --git a/services/main_config_loader.go b/services/main_config_loader.go
index 48f0892..274663b 100644
--- a/services/main_config_loader.go
+++ b/services/main_config_loader.go
@@ -9,8 +9,8 @@ import (
 	"github.com/google/go-github/v48/github"
 	"gopkg.in/yaml.v3"
 
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
-	"github.com/mongodb/code-example-tooling/code-copier/types"
+	"github.com/grove-platform/github-copier/configs"
+	"github.com/grove-platform/github-copier/types"
 )
 
 // DefaultMainConfigLoader implements the ConfigLoader interface with main config support
@@ -246,6 +246,9 @@ func (mcl *DefaultMainConfigLoader) loadLocalWorkflowConfig(ctx context.Context,
 	if err != nil {
 		return nil, fmt.Errorf("failed to get workflow config file: %w", err)
 	}
+	if fileContent == nil {
+		return nil, fmt.Errorf("workflow config file content is nil for path: %s", ref.Path)
+	}
 
 	content, err = fileContent.GetContent()
 	if err != nil {
@@ -295,6 +298,9 @@ func (mcl *DefaultMainConfigLoader) loadRemoteWorkflowConfig(ctx context.Context
 	if err != nil {
 		return nil, fmt.Errorf("failed to get workflow config file from %s: %w", ref.Repo, err)
 	}
+	if fileContent == nil {
+		return nil, fmt.Errorf("workflow config file content is nil for path: %s in repo %s", ref.Path, ref.Repo)
+	}
 
 	content, err := fileContent.GetContent()
 	if err != nil {
@@ -415,7 +421,7 @@ func (mcl *DefaultMainConfigLoader) resolveReference(ctx context.Context, ref st
 	// Supports:
 	// - Relative paths: "strategies/pr-strategy.yaml"
 	// - Repo references: "repo://owner/repo/path/to/file.yaml@branch"
-	
+
 	if strings.HasPrefix(ref, "repo://") {
 		// Remote repo reference
 		return mcl.resolveRemoteReference(ctx, ref)
@@ -429,7 +435,7 @@ func (mcl *DefaultMainConfigLoader) resolveReference(ctx context.Context, ref st
 func (mcl *DefaultMainConfigLoader) resolveRemoteReference(ctx context.Context, ref string) (string, error) {
 	// Parse: repo://owner/repo/path/to/file.yaml@branch
 	ref = strings.TrimPrefix(ref, "repo://")
-	
+
 	// Split by @ to get branch
 	parts := strings.Split(ref, "@")
 	branch := "main"
@@ -466,6 +472,9 @@ func (mcl *DefaultMainConfigLoader) resolveRemoteReference(ctx context.Context,
 	if err != nil {
 		return "", fmt.Errorf("failed to get referenced file: %w", err)
 	}
+	if fileContent == nil {
+		return "", fmt.Errorf("referenced file content is nil for path: %s", filePath)
+	}
 
 	return fileContent.GetContent()
 }
@@ -502,7 +511,9 @@ func (mcl *DefaultMainConfigLoader) resolveRelativeReference(ctx context.Context
 	if err != nil {
 		return "", fmt.Errorf("failed to get referenced file: %w", err)
 	}
+	if fileContent == nil {
+		return "", fmt.Errorf("referenced file content is nil for path: %s", resolvedPath)
+	}
 
 	return fileContent.GetContent()
 }
-
diff --git a/services/main_config_loader_test.go b/services/main_config_loader_test.go
index 7c5cc56..eab8f3a 100644
--- a/services/main_config_loader_test.go
+++ b/services/main_config_loader_test.go
@@ -8,9 +8,9 @@ import (
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
-	"github.com/mongodb/code-example-tooling/code-copier/services"
-	test "github.com/mongodb/code-example-tooling/code-copier/tests"
+	"github.com/grove-platform/github-copier/configs"
+	"github.com/grove-platform/github-copier/services"
+	test "github.com/grove-platform/github-copier/tests"
 )
 
 // Helper to encode YAML content to base64 for main config tests
@@ -980,4 +980,3 @@ workflow_configs:
 	assert.Equal(t, "mongodb/working-repo", workflow.Source.Repo)
 	assert.Equal(t, "mongodb/dest-repo", workflow.Destination.Repo)
 }
-
diff --git a/services/pattern_matcher.go b/services/pattern_matcher.go
index 46e1026..ee3feb0 100644
--- a/services/pattern_matcher.go
+++ b/services/pattern_matcher.go
@@ -7,7 +7,7 @@ import (
 	"strings"
 
 	"github.com/bmatcuk/doublestar/v4"
-	"github.com/mongodb/code-example-tooling/code-copier/types"
+	"github.com/grove-platform/github-copier/types"
 )
 
 // PatternMatcher handles pattern matching for file paths
@@ -56,20 +56,20 @@ func (pm *DefaultPatternMatcher) Match(filePath string, pattern types.SourcePatt
 func (pm *DefaultPatternMatcher) matchPrefix(filePath, pattern string) types.MatchResult {
 	// Normalize paths (remove trailing slashes)
 	pattern = strings.TrimSuffix(pattern, "/")
-	
+
 	if strings.HasPrefix(filePath, pattern) {
 		// Extract the relative path after the prefix
 		relPath := strings.TrimPrefix(filePath, pattern)
 		relPath = strings.TrimPrefix(relPath, "/")
-		
+
 		variables := map[string]string{
 			"matched_prefix": pattern,
 			"relative_path":  relPath,
 		}
-		
+
 		return types.NewMatchResult(true, variables)
 	}
-	
+
 	return types.NewMatchResult(false, nil)
 }
 
@@ -95,8 +95,6 @@ func (pm *DefaultPatternMatcher) matchGlob(filePath, pattern string) types.Match
 	return types.NewMatchResult(false, nil)
 }
 
-
-
 // matchRegex matches using regular expressions with named capture groups
 func (pm *DefaultPatternMatcher) matchRegex(filePath, pattern string) types.MatchResult {
 	re, err := regexp.Compile(pattern)
@@ -148,14 +146,14 @@ func (pt *DefaultPathTransformer) Transform(sourcePath string, template string,
 	// Create transformation context
 	ctx := types.NewTransformContext(sourcePath, variables)
 	ctx.AddBuiltInVariables()
-	
+
 	// Replace variables in template
 	result := template
 	for key, value := range ctx.Variables {
 		placeholder := fmt.Sprintf("${%s}", key)
 		result = strings.ReplaceAll(result, placeholder, value)
 	}
-	
+
 	// Check for unreplaced variables
 	if strings.Contains(result, "${") {
 		// Extract unreplaced variable names for better error message
@@ -164,7 +162,7 @@ func (pt *DefaultPathTransformer) Transform(sourcePath string, template string,
 			return "", fmt.Errorf("unreplaced variables in template: %v", unreplaced)
 		}
 	}
-	
+
 	return result, nil
 }
 
@@ -215,7 +213,7 @@ func (mt *DefaultMessageTemplater) RenderPRTitle(template string, ctx *types.Mes
 // RenderPRBody renders a PR body template
 func (mt *DefaultMessageTemplater) RenderPRBody(template string, ctx *types.MessageContext) string {
 	if template == "" {
-		return fmt.Sprintf("Automated update of %d file(s) from %s (PR #%d)", 
+		return fmt.Sprintf("Automated update of %d file(s) from %s (PR #%d)",
 			ctx.FileCount, ctx.SourceRepo, ctx.PRNumber)
 	}
 	return mt.render(template, ctx)
@@ -224,7 +222,7 @@ func (mt *DefaultMessageTemplater) RenderPRBody(template string, ctx *types.Mess
 // render performs the actual template rendering
 func (mt *DefaultMessageTemplater) render(template string, ctx *types.MessageContext) string {
 	result := template
-	
+
 	// Built-in context variables
 	replacements := map[string]string{
 		"${rule_name}":     ctx.RuleName,
@@ -236,18 +234,18 @@ func (mt *DefaultMessageTemplater) render(template string, ctx *types.MessageCon
 		"${pr_number}":     fmt.Sprintf("%d", ctx.PRNumber),
 		"${commit_sha}":    ctx.CommitSHA,
 	}
-	
+
 	// Apply built-in replacements
 	for placeholder, value := range replacements {
 		result = strings.ReplaceAll(result, placeholder, value)
 	}
-	
+
 	// Apply custom variables from pattern matching
 	for key, value := range ctx.Variables {
 		placeholder := fmt.Sprintf("${%s}", key)
 		result = strings.ReplaceAll(result, placeholder, value)
 	}
-	
+
 	return result
 }
 
@@ -273,4 +271,3 @@ func (pm *DefaultPatternMatcher) shouldExclude(filePath string, excludePatterns
 
 	return false
 }
-
diff --git a/services/pattern_matcher_test.go b/services/pattern_matcher_test.go
index c999a64..90dbf29 100644
--- a/services/pattern_matcher_test.go
+++ b/services/pattern_matcher_test.go
@@ -3,8 +3,8 @@ package services_test
 import (
 	"testing"
 
-	"github.com/mongodb/code-example-tooling/code-copier/services"
-	"github.com/mongodb/code-example-tooling/code-copier/types"
+	"github.com/grove-platform/github-copier/services"
+	"github.com/grove-platform/github-copier/types"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 )
@@ -13,9 +13,9 @@ func TestPatternMatcher_Prefix(t *testing.T) {
 	matcher := services.NewPatternMatcher()
 
 	tests := []struct {
-		name     string
-		pattern  types.SourcePattern
-		filePath string
+		name      string
+		pattern   types.SourcePattern
+		filePath  string
 		wantMatch bool
 	}{
 		{
diff --git a/services/service_container.go b/services/service_container.go
index a112eab..e9b6879 100644
--- a/services/service_container.go
+++ b/services/service_container.go
@@ -3,9 +3,10 @@ package services
 import (
 	"context"
 	"fmt"
+	"sync"
 	"time"
 
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
+	"github.com/grove-platform/github-copier/configs"
 )
 
 // ServiceContainer holds all application services with dependency injection
@@ -25,6 +26,10 @@ type ServiceContainer struct {
 
 	// Server state
 	StartTime time.Time
+
+	// Shutdown state
+	closeOnce sync.Once
+	closed    bool
 }
 
 // NewServiceContainer creates and initializes all services
@@ -84,10 +89,19 @@ func NewServiceContainer(config *configs.Config) (*ServiceContainer, error) {
 	}, nil
 }
 
-// Close cleans up resources
+// Close cleans up resources. Safe to call multiple times.
 func (sc *ServiceContainer) Close(ctx context.Context) error {
-	if sc.AuditLogger != nil {
-		return sc.AuditLogger.Close(ctx)
-	}
-	return nil
+	var closeErr error
+	sc.closeOnce.Do(func() {
+		if sc.AuditLogger != nil {
+			closeErr = sc.AuditLogger.Close(ctx)
+		}
+		sc.closed = true
+	})
+	return closeErr
+}
+
+// IsClosed returns true if the container has been closed
+func (sc *ServiceContainer) IsClosed() bool {
+	return sc.closed
 }
diff --git a/services/service_container_test.go b/services/service_container_test.go
index b230bfb..ed8bcc7 100644
--- a/services/service_container_test.go
+++ b/services/service_container_test.go
@@ -5,7 +5,7 @@ import (
 	"testing"
 	"time"
 
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
+	"github.com/grove-platform/github-copier/configs"
 )
 
 func TestNewServiceContainer(t *testing.T) {
@@ -46,7 +46,7 @@ func TestNewServiceContainer(t *testing.T) {
 				ConfigRepoOwner: "test-owner",
 				ConfigRepoName:  "test-repo",
 				AuditEnabled:    true,
-				MongoURI:       "",
+				MongoURI:        "",
 			},
 			wantErr:       true,
 			checkServices: false,
@@ -126,9 +126,9 @@ func TestNewServiceContainer(t *testing.T) {
 
 func TestServiceContainer_Close(t *testing.T) {
 	tests := []struct {
-		name        string
-		config      *configs.Config
-		wantErr     bool
+		name    string
+		config  *configs.Config
+		wantErr bool
 	}{
 		{
 			name: "close with NoOp audit logger",
@@ -196,12 +196,12 @@ func TestServiceContainer_ConfigPropagation(t *testing.T) {
 
 func TestServiceContainer_SlackNotifierConfiguration(t *testing.T) {
 	tests := []struct {
-		name            string
-		webhookURL      string
-		channel         string
-		username        string
-		iconEmoji       string
-		wantEnabled     bool
+		name        string
+		webhookURL  string
+		channel     string
+		username    string
+		iconEmoji   string
+		wantEnabled bool
 	}{
 		{
 			name:        "Slack enabled",
@@ -276,8 +276,8 @@ func TestServiceContainer_AuditLoggerConfiguration(t *testing.T) {
 				ConfigRepoOwner: "test-owner",
 				ConfigRepoName:  "test-repo",
 				AuditEnabled:    tt.auditEnabled,
-				MongoURI:       tt.mongoURI,
-				AuditDatabase:  "test-db",
+				MongoURI:        tt.mongoURI,
+				AuditDatabase:   "test-db",
 				AuditCollection: "test-coll",
 			}
 
@@ -357,4 +357,3 @@ func TestServiceContainer_StartTimeTracking(t *testing.T) {
 		t.Error("StartTime is after container creation")
 	}
 }
-
diff --git a/services/slack_notifier_test.go b/services/slack_notifier_test.go
index 03b7655..6dd9030 100644
--- a/services/slack_notifier_test.go
+++ b/services/slack_notifier_test.go
@@ -13,27 +13,27 @@ import (
 
 func TestNewSlackNotifier(t *testing.T) {
 	tests := []struct {
-		name       string
-		webhookURL string
-		channel    string
-		username   string
-		iconEmoji  string
+		name        string
+		webhookURL  string
+		channel     string
+		username    string
+		iconEmoji   string
 		wantEnabled bool
 	}{
 		{
-			name:       "enabled with webhook URL",
-			webhookURL: "https://hooks.slack.com/services/TEST",
-			channel:    "#test",
-			username:   "Test Bot",
-			iconEmoji:  ":robot:",
+			name:        "enabled with webhook URL",
+			webhookURL:  "https://hooks.slack.com/services/TEST",
+			channel:     "#test",
+			username:    "Test Bot",
+			iconEmoji:   ":robot:",
 			wantEnabled: true,
 		},
 		{
-			name:       "disabled without webhook URL",
-			webhookURL: "",
-			channel:    "#test",
-			username:   "Test Bot",
-			iconEmoji:  ":robot:",
+			name:        "disabled without webhook URL",
+			webhookURL:  "",
+			channel:     "#test",
+			username:    "Test Bot",
+			iconEmoji:   ":robot:",
 			wantEnabled: false,
 		},
 	}
@@ -93,7 +93,7 @@ func TestSlackNotifier_NotifyPRProcessed(t *testing.T) {
 			var receivedMessage *SlackMessage
 			server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
 				body, _ := io.ReadAll(r.Body)
-				json.Unmarshal(body, &receivedMessage)
+				_ = json.Unmarshal(body, &receivedMessage)
 				w.WriteHeader(http.StatusOK)
 			}))
 			defer server.Close()
@@ -138,7 +138,7 @@ func TestSlackNotifier_NotifyError(t *testing.T) {
 	var receivedMessage *SlackMessage
 	server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
 		body, _ := io.ReadAll(r.Body)
-		json.Unmarshal(body, &receivedMessage)
+		_ = json.Unmarshal(body, &receivedMessage)
 		w.WriteHeader(http.StatusOK)
 	}))
 	defer server.Close()
@@ -171,18 +171,18 @@ func TestSlackNotifier_NotifyError(t *testing.T) {
 
 func TestSlackNotifier_NotifyFilesCopied(t *testing.T) {
 	tests := []struct {
-		name      string
-		fileCount int
+		name          string
+		fileCount     int
 		wantTruncated bool
 	}{
 		{
-			name:      "few files",
-			fileCount: 5,
+			name:          "few files",
+			fileCount:     5,
 			wantTruncated: false,
 		},
 		{
-			name:      "many files",
-			fileCount: 15,
+			name:          "many files",
+			fileCount:     15,
 			wantTruncated: true,
 		},
 	}
@@ -206,7 +206,7 @@ func TestSlackNotifier_NotifyFilesCopied(t *testing.T) {
 			var receivedMessage *SlackMessage
 			server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
 				body, _ := io.ReadAll(r.Body)
-				json.Unmarshal(body, &receivedMessage)
+				_ = json.Unmarshal(body, &receivedMessage)
 				w.WriteHeader(http.StatusOK)
 			}))
 			defer server.Close()
@@ -245,7 +245,7 @@ func TestSlackNotifier_NotifyDeprecation(t *testing.T) {
 	var receivedMessage *SlackMessage
 	server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
 		body, _ := io.ReadAll(r.Body)
-		json.Unmarshal(body, &receivedMessage)
+		_ = json.Unmarshal(body, &receivedMessage)
 		w.WriteHeader(http.StatusOK)
 	}))
 	defer server.Close()
@@ -329,4 +329,3 @@ func containsMiddle(s, substr string) bool {
 	}
 	return false
 }
-
diff --git a/services/webhook_handler_new.go b/services/webhook_handler_new.go
index 8d090e7..dd7ec04 100644
--- a/services/webhook_handler_new.go
+++ b/services/webhook_handler_new.go
@@ -12,8 +12,8 @@ import (
 	"time"
 
 	"github.com/google/go-github/v48/github"
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
-	"github.com/mongodb/code-example-tooling/code-copier/types"
+	"github.com/grove-platform/github-copier/configs"
+	"github.com/grove-platform/github-copier/types"
 )
 
 const (
@@ -184,7 +184,7 @@ func HandleWebhookWithContainer(w http.ResponseWriter, r *http.Request, config *
 
 	w.Header().Set("Content-Type", "application/json")
 	w.WriteHeader(http.StatusAccepted)
-	w.Write([]byte(`{"status":"accepted"}`))
+	_, _ = w.Write([]byte(`{"status":"accepted"}`))
 
 	LogInfoCtx(ctx, "response sent", map[string]interface{}{
 		"elapsed_ms": time.Since(startTime).Milliseconds(),
@@ -210,7 +210,11 @@ func handleMergedPRWithContainer(ctx context.Context, prNumber int, sourceCommit
 
 	// Configure GitHub permissions
 	if InstallationAccessToken == "" {
-		ConfigurePermissions()
+		if err := ConfigurePermissions(); err != nil {
+			LogAndReturnError(ctx, "auth", "failed to configure GitHub permissions", err)
+			container.MetricsCollector.RecordWebhookFailed()
+			return
+		}
 	}
 
 	// Load configuration using new loader
@@ -222,7 +226,7 @@ func handleMergedPRWithContainer(ctx context.Context, prNumber int, sourceCommit
 		container.MetricsCollector.RecordWebhookFailed()
 
 		// Send error notification to Slack
-		container.SlackNotifier.NotifyError(ctx, &ErrorEvent{
+		_ = container.SlackNotifier.NotifyError(ctx, &ErrorEvent{
 			Operation:  "config_load",
 			Error:      err,
 			PRNumber:   prNumber,
@@ -267,7 +271,7 @@ func handleMergedPRWithContainer(ctx context.Context, prNumber int, sourceCommit
 		container.MetricsCollector.RecordWebhookFailed()
 
 		// Send error notification to Slack
-		container.SlackNotifier.NotifyError(ctx, &ErrorEvent{
+		_ = container.SlackNotifier.NotifyError(ctx, &ErrorEvent{
 			Operation:  "get_files",
 			Error:      err,
 			PRNumber:   prNumber,
@@ -294,12 +298,16 @@ func handleMergedPRWithContainer(ctx context.Context, prNumber int, sourceCommit
 	container.FileStateService.ClearFilesToUpload()
 
 	// Update deprecation file - copy from FileStateService to global map for legacy function
+	// The deprecationMap is keyed by deprecation file name, with a slice of entries per file
 	deprecationMap := container.FileStateService.GetFilesToDeprecate()
 	FilesToDeprecate = make(map[string]types.Configs)
-	for _, entry := range deprecationMap {
-		FilesToDeprecate[entry.FileName] = types.Configs{
-			TargetRepo:   entry.Repo,
-			TargetBranch: entry.Branch,
+	for _, entries := range deprecationMap {
+		// Iterate over all entries for each deprecation file
+		for _, entry := range entries {
+			FilesToDeprecate[entry.FileName] = types.Configs{
+				TargetRepo:   entry.Repo,
+				TargetBranch: entry.Branch,
+			}
 		}
 	}
 	UpdateDeprecationFile()
@@ -317,7 +325,7 @@ func handleMergedPRWithContainer(ctx context.Context, prNumber int, sourceCommit
 	})
 
 	// Send success notification to Slack
-	container.SlackNotifier.NotifyPRProcessed(ctx, &PRProcessedEvent{
+	_ = container.SlackNotifier.NotifyPRProcessed(ctx, &PRProcessedEvent{
 		PRNumber:       prNumber,
 		PRTitle:        fmt.Sprintf("PR #%d", prNumber), // TODO: Get actual PR title from GitHub
 		PRURL:          fmt.Sprintf("https://github.com/%s/pull/%d", webhookRepo, prNumber),
diff --git a/services/webhook_handler_new_test.go b/services/webhook_handler_new_test.go
index 1f0e129..d488ac3 100644
--- a/services/webhook_handler_new_test.go
+++ b/services/webhook_handler_new_test.go
@@ -17,7 +17,7 @@ import (
 	"testing"
 
 	"github.com/google/go-github/v48/github"
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
+	"github.com/grove-platform/github-copier/configs"
 )
 
 func TestSimpleVerifySignature(t *testing.T) {
@@ -87,8 +87,8 @@ func TestHandleWebhookWithContainer_MissingEventType(t *testing.T) {
 	config := &configs.Config{
 		ConfigRepoOwner: "test-owner",
 		ConfigRepoName:  "test-repo",
-		
-		AuditEnabled:   false,
+
+		AuditEnabled: false,
 	}
 
 	container, err := NewServiceContainer(config)
@@ -117,9 +117,9 @@ func TestHandleWebhookWithContainer_InvalidSignature(t *testing.T) {
 	config := &configs.Config{
 		ConfigRepoOwner: "test-owner",
 		ConfigRepoName:  "test-repo",
-		
-		WebhookSecret:  "test-secret",
-		AuditEnabled:   false,
+
+		WebhookSecret: "test-secret",
+		AuditEnabled:  false,
 	}
 
 	container, err := NewServiceContainer(config)
@@ -146,9 +146,9 @@ func TestHandleWebhookWithContainer_ValidSignature(t *testing.T) {
 	config := &configs.Config{
 		ConfigRepoOwner: "test-owner",
 		ConfigRepoName:  "test-repo",
-		
-		WebhookSecret:  secret,
-		AuditEnabled:   false,
+
+		WebhookSecret: secret,
+		AuditEnabled:  false,
 	}
 
 	container, err := NewServiceContainer(config)
@@ -190,8 +190,8 @@ func TestHandleWebhookWithContainer_NonPREvent(t *testing.T) {
 	config := &configs.Config{
 		ConfigRepoOwner: "test-owner",
 		ConfigRepoName:  "test-repo",
-		
-		AuditEnabled:   false,
+
+		AuditEnabled: false,
 	}
 
 	container, err := NewServiceContainer(config)
@@ -222,8 +222,8 @@ func TestHandleWebhookWithContainer_NonMergedPR(t *testing.T) {
 	config := &configs.Config{
 		ConfigRepoOwner: "test-owner",
 		ConfigRepoName:  "test-repo",
-		
-		AuditEnabled:   false,
+
+		AuditEnabled: false,
 	}
 
 	container, err := NewServiceContainer(config)
@@ -328,7 +328,7 @@ func TestHandleWebhookWithContainer_MergedPR(t *testing.T) {
 
 	// Check response body
 	var response map[string]string
-	json.Unmarshal(w.Body.Bytes(), &response)
+	_ = json.Unmarshal(w.Body.Bytes(), &response)
 	if response["status"] != "accepted" {
 		t.Errorf("Response status = %v, want accepted", response["status"])
 	}
@@ -404,7 +404,7 @@ func TestHandleWebhookWithContainer_MergedPRToDevelopmentBranch(t *testing.T) {
 
 	// Check response body
 	var response map[string]string
-	json.Unmarshal(w.Body.Bytes(), &response)
+	_ = json.Unmarshal(w.Body.Bytes(), &response)
 	if response["status"] != "accepted" {
 		t.Errorf("Response status = %v, want accepted", response["status"])
 	}
@@ -509,7 +509,7 @@ func TestHandleWebhookWithContainer_MergedPRWithDifferentBranches(t *testing.T)
 
 			// Check response body
 			var response map[string]string
-			json.Unmarshal(w.Body.Bytes(), &response)
+			_ = json.Unmarshal(w.Body.Bytes(), &response)
 			if response["status"] != "accepted" {
 				t.Errorf("Response status = %v, want accepted", response["status"])
 			}
@@ -543,4 +543,3 @@ func TestStatusDeleted(t *testing.T) {
 		t.Errorf("statusDeleted = %s, want DELETED", statusDeleted)
 	}
 }
-
diff --git a/services/workflow_processor.go b/services/workflow_processor.go
index 86cf222..a766907 100644
--- a/services/workflow_processor.go
+++ b/services/workflow_processor.go
@@ -9,7 +9,7 @@ import (
 
 	"github.com/bmatcuk/doublestar/v4"
 	"github.com/google/go-github/v48/github"
-	. "github.com/mongodb/code-example-tooling/code-copier/types"
+	. "github.com/grove-platform/github-copier/types"
 )
 
 // WorkflowProcessor processes workflows and applies transformations
@@ -52,10 +52,10 @@ func (wp *workflowProcessor) ProcessWorkflow(
 	sourceCommitSHA string,
 ) error {
 	LogInfoCtx(ctx, "Processing workflow", map[string]interface{}{
-		"workflow_name":   workflow.Name,
-		"source_repo":     workflow.Source.Repo,
+		"workflow_name":    workflow.Name,
+		"source_repo":      workflow.Source.Repo,
 		"destination_repo": workflow.Destination.Repo,
-		"file_count":      len(changedFiles),
+		"file_count":       len(changedFiles),
 	})
 
 	// Track files matched and skipped
@@ -81,9 +81,9 @@ func (wp *workflowProcessor) ProcessWorkflow(
 	}
 
 	LogInfoCtx(ctx, "Workflow processing complete", map[string]interface{}{
-		"workflow_name":  workflow.Name,
-		"files_matched":  filesMatched,
-		"files_skipped":  filesSkipped,
+		"workflow_name": workflow.Name,
+		"files_matched": filesMatched,
+		"files_skipped": filesSkipped,
 	})
 
 	return nil
@@ -119,15 +119,16 @@ func (wp *workflowProcessor) processFileForWorkflow(
 
 		// File matched this transformation
 		LogInfoCtx(ctx, "File matched transformation", map[string]interface{}{
-			"workflow_name":      workflow.Name,
-			"transformation_idx": i,
+			"workflow_name":       workflow.Name,
+			"transformation_idx":  i,
 			"transformation_type": transformation.GetType(),
-			"source_path":        file.Path,
-			"target_path":        targetPath,
+			"source_path":         file.Path,
+			"target_path":         targetPath,
 		})
 
 		// Handle file based on status
-		if file.Status == "removed" {
+		// GitHub GraphQL API returns uppercase status: "DELETED", "ADDED", "MODIFIED", etc.
+		if file.Status == "DELETED" || file.Status == "removed" {
 			// Add to deprecation map
 			wp.addToDeprecationMap(workflow, targetPath)
 		} else {
@@ -178,12 +179,12 @@ func (wp *workflowProcessor) applyMoveTransformation(
 ) (matched bool, targetPath string, err error) {
 	// Check if source path starts with the "from" prefix
 	from := strings.TrimSuffix(move.From, "/")
-	
+
 	if sourcePath == from {
 		// Exact match - move the file to the "to" path
 		return true, move.To, nil
 	}
-	
+
 	if strings.HasPrefix(sourcePath, from+"/") {
 		// Path is under the "from" directory - preserve relative path
 		relativePath := strings.TrimPrefix(sourcePath, from+"/")
@@ -242,7 +243,7 @@ func (wp *workflowProcessor) applyRegexTransformation(
 		Type:    PatternTypeRegex,
 		Pattern: regex.Pattern,
 	}
-	
+
 	matchResult := wp.patternMatcher.Match(sourcePath, sourcePattern)
 	if !matchResult.Matched {
 		return false, "", nil
@@ -260,11 +261,11 @@ func (wp *workflowProcessor) applyRegexTransformation(
 // extractGlobVariables extracts variables from a glob pattern match
 func (wp *workflowProcessor) extractGlobVariables(pattern, path string) map[string]string {
 	variables := make(map[string]string)
-	
+
 	// Extract common variables
 	// For pattern "mflix/server/**" matching "mflix/server/java-spring/src/main.java"
 	// Extract relative_path = "java-spring/src/main.java"
-	
+
 	// Find the ** in the pattern
 	starStarIdx := strings.Index(pattern, "**")
 	if starStarIdx >= 0 {
@@ -275,7 +276,7 @@ func (wp *workflowProcessor) extractGlobVariables(pattern, path string) map[stri
 			variables["relative_path"] = relativePath
 		}
 	}
-	
+
 	return variables
 }
 
@@ -406,27 +407,6 @@ func getCommitStrategyType(workflow Workflow) string {
 	return "pull_request" // default
 }
 
-func getCommitMessage(workflow Workflow) string {
-	if workflow.CommitStrategy != nil && workflow.CommitStrategy.CommitMessage != "" {
-		return workflow.CommitStrategy.CommitMessage
-	}
-	return fmt.Sprintf("Update from workflow: %s", workflow.Name)
-}
-
-func getPRTitle(workflow Workflow) string {
-	if workflow.CommitStrategy != nil && workflow.CommitStrategy.PRTitle != "" {
-		return workflow.CommitStrategy.PRTitle
-	}
-	return getCommitMessage(workflow)
-}
-
-func getPRBody(workflow Workflow) string {
-	if workflow.CommitStrategy != nil && workflow.CommitStrategy.PRBody != "" {
-		return workflow.CommitStrategy.PRBody
-	}
-	return ""
-}
-
 func getUsePRTemplate(workflow Workflow) bool {
 	if workflow.CommitStrategy != nil {
 		return workflow.CommitStrategy.UsePRTemplate
diff --git a/services/workflow_processor_test.go b/services/workflow_processor_test.go
new file mode 100644
index 0000000..6ea30db
--- /dev/null
+++ b/services/workflow_processor_test.go
@@ -0,0 +1,833 @@
+package services_test
+
+import (
+	"context"
+	"testing"
+
+	"github.com/grove-platform/github-copier/services"
+	"github.com/grove-platform/github-copier/types"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+// ============================================================================
+// Mock implementations
+// ============================================================================
+
+// mockMessageTemplater is a mock implementation of MessageTemplater
+type mockMessageTemplater struct{}
+
+func (m *mockMessageTemplater) RenderCommitMessage(template string, ctx *types.MessageContext) string {
+	if template == "" {
+		return "Default commit message"
+	}
+	return template
+}
+
+func (m *mockMessageTemplater) RenderPRTitle(template string, ctx *types.MessageContext) string {
+	if template == "" {
+		return "Default PR title"
+	}
+	return template
+}
+
+func (m *mockMessageTemplater) RenderPRBody(template string, ctx *types.MessageContext) string {
+	if template == "" {
+		return "Default PR body"
+	}
+	return template
+}
+
+// ============================================================================
+// Test helper functions
+// ============================================================================
+
+func createTestWorkflow(name string, transformations []types.Transformation) types.Workflow {
+	return types.Workflow{
+		Name: name,
+		Source: types.Source{
+			Repo:   "test-org/source-repo",
+			Branch: "main",
+		},
+		Destination: types.Destination{
+			Repo:   "test-org/dest-repo",
+			Branch: "main",
+		},
+		Transformations: transformations,
+	}
+}
+
+func createMoveTransformation(from, to string) types.Transformation {
+	return types.Transformation{
+		Move: &types.MoveTransform{From: from, To: to},
+	}
+}
+
+func createCopyTransformation(from, to string) types.Transformation {
+	return types.Transformation{
+		Copy: &types.CopyTransform{From: from, To: to},
+	}
+}
+
+func createGlobTransformation(pattern, transform string) types.Transformation {
+	return types.Transformation{
+		Glob: &types.GlobTransform{Pattern: pattern, Transform: transform},
+	}
+}
+
+func createRegexTransformation(pattern, transform string) types.Transformation {
+	return types.Transformation{
+		Regex: &types.RegexTransform{Pattern: pattern, Transform: transform},
+	}
+}
+
+// ============================================================================
+// Tests for Move Transformation
+// ============================================================================
+
+func TestWorkflowProcessor_MoveTransformation(t *testing.T) {
+	tests := []struct {
+		name       string
+		from       string
+		to         string
+		sourcePath string
+		wantMatch  bool
+		wantTarget string
+	}{
+		{
+			name:       "simple directory move",
+			from:       "src",
+			to:         "dest",
+			sourcePath: "src/file.go",
+			wantMatch:  true,
+			wantTarget: "dest/file.go",
+		},
+		{
+			name:       "nested directory move",
+			from:       "examples/go",
+			to:         "code/golang",
+			sourcePath: "examples/go/main.go",
+			wantMatch:  true,
+			wantTarget: "code/golang/main.go",
+		},
+		{
+			name:       "deeply nested path",
+			from:       "src",
+			to:         "dest",
+			sourcePath: "src/pkg/internal/utils/helper.go",
+			wantMatch:  true,
+			wantTarget: "dest/pkg/internal/utils/helper.go",
+		},
+		{
+			name:       "exact file match",
+			from:       "README.md",
+			to:         "docs/README.md",
+			sourcePath: "README.md",
+			wantMatch:  true,
+			wantTarget: "docs/README.md",
+		},
+		{
+			name:       "no match - different prefix",
+			from:       "src",
+			to:         "dest",
+			sourcePath: "other/file.go",
+			wantMatch:  false,
+			wantTarget: "",
+		},
+		{
+			name:       "no match - partial prefix",
+			from:       "src",
+			to:         "dest",
+			sourcePath: "srcfile.go",
+			wantMatch:  false,
+			wantTarget: "",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			// Create processor with real implementations for move (doesn't need mocks)
+			fileStateService := services.NewFileStateService()
+			processor := services.NewWorkflowProcessor(
+				services.NewPatternMatcher(),
+				services.NewPathTransformer(),
+				fileStateService,
+				nil, // metrics collector
+				&mockMessageTemplater{},
+			)
+
+			workflow := createTestWorkflow("test-workflow", []types.Transformation{
+				createMoveTransformation(tt.from, tt.to),
+			})
+
+			// Create a removed file to avoid GitHub API calls
+			changedFiles := []types.ChangedFile{
+				{Path: tt.sourcePath, Status: "removed"},
+			}
+
+			err := processor.ProcessWorkflow(context.Background(), workflow, changedFiles, 1, "abc123")
+			require.NoError(t, err)
+
+			// Check deprecation map for removed files
+			deprecated := fileStateService.GetFilesToDeprecate()
+			if tt.wantMatch {
+				assert.NotEmpty(t, deprecated, "expected file to be added to deprecation map")
+			} else {
+				assert.Empty(t, deprecated, "expected no files in deprecation map")
+			}
+		})
+	}
+}
+
+// ============================================================================
+// Tests for Copy Transformation
+// ============================================================================
+
+func TestWorkflowProcessor_CopyTransformation(t *testing.T) {
+	tests := []struct {
+		name       string
+		from       string
+		to         string
+		sourcePath string
+		wantMatch  bool
+	}{
+		{
+			name:       "exact file copy",
+			from:       "config.yaml",
+			to:         "settings/config.yaml",
+			sourcePath: "config.yaml",
+			wantMatch:  true,
+		},
+		{
+			name:       "nested file copy",
+			from:       "src/main.go",
+			to:         "app/main.go",
+			sourcePath: "src/main.go",
+			wantMatch:  true,
+		},
+		{
+			name:       "no match - different file",
+			from:       "config.yaml",
+			to:         "settings/config.yaml",
+			sourcePath: "other.yaml",
+			wantMatch:  false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			fileStateService := services.NewFileStateService()
+			processor := services.NewWorkflowProcessor(
+				services.NewPatternMatcher(),
+				services.NewPathTransformer(),
+				fileStateService,
+				nil,
+				&mockMessageTemplater{},
+			)
+
+			workflow := createTestWorkflow("test-workflow", []types.Transformation{
+				createCopyTransformation(tt.from, tt.to),
+			})
+
+			changedFiles := []types.ChangedFile{
+				{Path: tt.sourcePath, Status: "removed"},
+			}
+
+			err := processor.ProcessWorkflow(context.Background(), workflow, changedFiles, 1, "abc123")
+			require.NoError(t, err)
+
+			deprecated := fileStateService.GetFilesToDeprecate()
+			if tt.wantMatch {
+				assert.NotEmpty(t, deprecated, "expected file to be added to deprecation map")
+			} else {
+				assert.Empty(t, deprecated, "expected no files in deprecation map")
+			}
+		})
+	}
+}
+
+// ============================================================================
+// Tests for Glob Transformation
+// ============================================================================
+
+func TestWorkflowProcessor_GlobTransformation(t *testing.T) {
+	tests := []struct {
+		name       string
+		pattern    string
+		transform  string
+		sourcePath string
+		wantMatch  bool
+	}{
+		{
+			name:       "simple glob pattern",
+			pattern:    "src/**/*.go",
+			transform:  "dest/${relative_path}",
+			sourcePath: "src/main.go",
+			wantMatch:  true,
+		},
+		{
+			name:       "nested glob pattern",
+			pattern:    "examples/**/*.js",
+			transform:  "code/${relative_path}",
+			sourcePath: "examples/app/index.js",
+			wantMatch:  true,
+		},
+		{
+			name:       "no match - wrong extension",
+			pattern:    "src/**/*.go",
+			transform:  "dest/${relative_path}",
+			sourcePath: "src/main.py",
+			wantMatch:  false,
+		},
+		{
+			name:       "no match - wrong directory",
+			pattern:    "src/**/*.go",
+			transform:  "dest/${relative_path}",
+			sourcePath: "other/main.go",
+			wantMatch:  false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			fileStateService := services.NewFileStateService()
+			processor := services.NewWorkflowProcessor(
+				services.NewPatternMatcher(),
+				services.NewPathTransformer(),
+				fileStateService,
+				nil,
+				&mockMessageTemplater{},
+			)
+
+			workflow := createTestWorkflow("test-workflow", []types.Transformation{
+				createGlobTransformation(tt.pattern, tt.transform),
+			})
+
+			changedFiles := []types.ChangedFile{
+				{Path: tt.sourcePath, Status: "removed"},
+			}
+
+			err := processor.ProcessWorkflow(context.Background(), workflow, changedFiles, 1, "abc123")
+			require.NoError(t, err)
+
+			deprecated := fileStateService.GetFilesToDeprecate()
+			if tt.wantMatch {
+				assert.NotEmpty(t, deprecated, "expected file to be added to deprecation map")
+			} else {
+				assert.Empty(t, deprecated, "expected no files in deprecation map")
+			}
+		})
+	}
+}
+
+// ============================================================================
+// Tests for Regex Transformation
+// ============================================================================
+
+func TestWorkflowProcessor_RegexTransformation(t *testing.T) {
+	tests := []struct {
+		name       string
+		pattern    string
+		transform  string
+		sourcePath string
+		wantMatch  bool
+	}{
+		{
+			name:       "simple regex pattern",
+			pattern:    `^src/(?P<file>.+)\.go$`,
+			transform:  "dest/${file}.go",
+			sourcePath: "src/main.go",
+			wantMatch:  true,
+		},
+		{
+			name:       "regex with multiple groups",
+			pattern:    `^examples/(?P<lang>[^/]+)/(?P<file>.+)$`,
+			transform:  "code/${lang}/${file}",
+			sourcePath: "examples/go/main.go",
+			wantMatch:  true,
+		},
+		{
+			name:       "no match - pattern doesn't match",
+			pattern:    `^src/(?P<file>.+)\.go$`,
+			transform:  "dest/${file}.go",
+			sourcePath: "other/main.go",
+			wantMatch:  false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			fileStateService := services.NewFileStateService()
+			processor := services.NewWorkflowProcessor(
+				services.NewPatternMatcher(),
+				services.NewPathTransformer(),
+				fileStateService,
+				nil,
+				&mockMessageTemplater{},
+			)
+
+			workflow := createTestWorkflow("test-workflow", []types.Transformation{
+				createRegexTransformation(tt.pattern, tt.transform),
+			})
+
+			changedFiles := []types.ChangedFile{
+				{Path: tt.sourcePath, Status: "removed"},
+			}
+
+			err := processor.ProcessWorkflow(context.Background(), workflow, changedFiles, 1, "abc123")
+			require.NoError(t, err)
+
+			deprecated := fileStateService.GetFilesToDeprecate()
+			if tt.wantMatch {
+				assert.NotEmpty(t, deprecated, "expected file to be added to deprecation map")
+			} else {
+				assert.Empty(t, deprecated, "expected no files in deprecation map")
+			}
+		})
+	}
+}
+
+// ============================================================================
+// Tests for Exclude Patterns
+// ============================================================================
+
+func TestWorkflowProcessor_ExcludePatterns(t *testing.T) {
+	// Note: Exclude patterns use glob matching (doublestar), not regex
+	tests := []struct {
+		name         string
+		exclude      []string
+		sourcePath   string
+		wantExcluded bool
+	}{
+		{
+			name:         "exclude by extension glob",
+			exclude:      []string{"**/*_test.go"},
+			sourcePath:   "src/main_test.go",
+			wantExcluded: true,
+		},
+		{
+			name:         "exclude by directory glob",
+			exclude:      []string{"vendor/**"},
+			sourcePath:   "vendor/pkg/lib.go",
+			wantExcluded: true,
+		},
+		{
+			name:         "exclude by filename glob",
+			exclude:      []string{"**/.DS_Store"},
+			sourcePath:   "src/.DS_Store",
+			wantExcluded: true,
+		},
+		{
+			name:         "not excluded - no match",
+			exclude:      []string{"**/*_test.go"},
+			sourcePath:   "src/main.go",
+			wantExcluded: false,
+		},
+		{
+			name:         "multiple exclude patterns - first matches",
+			exclude:      []string{"**/*_test.go", "vendor/**"},
+			sourcePath:   "src/main_test.go",
+			wantExcluded: true,
+		},
+		{
+			name:         "multiple exclude patterns - second matches",
+			exclude:      []string{"**/*_test.go", "vendor/**"},
+			sourcePath:   "vendor/lib.go",
+			wantExcluded: true,
+		},
+		{
+			name:         "multiple exclude patterns - none match",
+			exclude:      []string{"**/*_test.go", "vendor/**"},
+			sourcePath:   "src/main.go",
+			wantExcluded: false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			fileStateService := services.NewFileStateService()
+			processor := services.NewWorkflowProcessor(
+				services.NewPatternMatcher(),
+				services.NewPathTransformer(),
+				fileStateService,
+				nil,
+				&mockMessageTemplater{},
+			)
+
+			workflow := types.Workflow{
+				Name: "test-workflow",
+				Source: types.Source{
+					Repo:   "test-org/source-repo",
+					Branch: "main",
+				},
+				Destination: types.Destination{
+					Repo:   "test-org/dest-repo",
+					Branch: "main",
+				},
+				Transformations: []types.Transformation{
+					createMoveTransformation("src", "dest"),
+					createMoveTransformation("vendor", "vendor"),
+				},
+				Exclude: tt.exclude,
+			}
+
+			changedFiles := []types.ChangedFile{
+				{Path: tt.sourcePath, Status: "removed"},
+			}
+
+			err := processor.ProcessWorkflow(context.Background(), workflow, changedFiles, 1, "abc123")
+			require.NoError(t, err)
+
+			deprecated := fileStateService.GetFilesToDeprecate()
+			if tt.wantExcluded {
+				assert.Empty(t, deprecated, "expected file to be excluded")
+			} else {
+				// Only check if the path matches a transformation
+				if tt.sourcePath == "src/main.go" {
+					assert.NotEmpty(t, deprecated, "expected file to be processed")
+				}
+			}
+		})
+	}
+}
+
+// ============================================================================
+// Tests for Multiple Transformations
+// ============================================================================
+
+func TestWorkflowProcessor_MultipleTransformations(t *testing.T) {
+	fileStateService := services.NewFileStateService()
+	processor := services.NewWorkflowProcessor(
+		services.NewPatternMatcher(),
+		services.NewPathTransformer(),
+		fileStateService,
+		nil,
+		&mockMessageTemplater{},
+	)
+
+	workflow := types.Workflow{
+		Name: "multi-transform-workflow",
+		Source: types.Source{
+			Repo:   "test-org/source-repo",
+			Branch: "main",
+		},
+		Destination: types.Destination{
+			Repo:   "test-org/dest-repo",
+			Branch: "main",
+		},
+		Transformations: []types.Transformation{
+			createMoveTransformation("src", "code"),
+			createMoveTransformation("docs", "documentation"),
+			createCopyTransformation("README.md", "docs/README.md"),
+		},
+	}
+
+	changedFiles := []types.ChangedFile{
+		{Path: "src/main.go", Status: "removed"},
+		{Path: "docs/guide.md", Status: "removed"},
+		{Path: "README.md", Status: "removed"},
+		{Path: "other/file.txt", Status: "removed"}, // Should not match
+	}
+
+	err := processor.ProcessWorkflow(context.Background(), workflow, changedFiles, 1, "abc123")
+	require.NoError(t, err)
+
+	deprecated := fileStateService.GetFilesToDeprecate()
+	assert.NotEmpty(t, deprecated, "expected files to be processed")
+
+	// Verify all 3 matching files are accumulated in the deprecation map
+	entries, exists := deprecated["deprecated_examples.json"]
+	assert.True(t, exists, "expected deprecation entry to exist")
+	require.Len(t, entries, 3, "expected 3 files to be accumulated (src/main.go, docs/guide.md, README.md)")
+
+	// Collect all file names
+	fileNames := make([]string, len(entries))
+	for i, e := range entries {
+		fileNames[i] = e.FileName
+	}
+
+	// Verify all expected files are present
+	assert.Contains(t, fileNames, "code/main.go", "expected src/main.go -> code/main.go")
+	assert.Contains(t, fileNames, "documentation/guide.md", "expected docs/guide.md -> documentation/guide.md")
+	assert.Contains(t, fileNames, "docs/README.md", "expected README.md -> docs/README.md")
+}
+
+// ============================================================================
+// Tests for Edge Cases
+// ============================================================================
+
+func TestWorkflowProcessor_EmptyChangedFiles(t *testing.T) {
+	fileStateService := services.NewFileStateService()
+	processor := services.NewWorkflowProcessor(
+		services.NewPatternMatcher(),
+		services.NewPathTransformer(),
+		fileStateService,
+		nil,
+		&mockMessageTemplater{},
+	)
+
+	workflow := createTestWorkflow("test-workflow", []types.Transformation{
+		createMoveTransformation("src", "dest"),
+	})
+
+	changedFiles := []types.ChangedFile{}
+
+	err := processor.ProcessWorkflow(context.Background(), workflow, changedFiles, 1, "abc123")
+	require.NoError(t, err)
+
+	deprecated := fileStateService.GetFilesToDeprecate()
+	assert.Empty(t, deprecated, "expected no files to be processed")
+}
+
+func TestWorkflowProcessor_NoTransformations(t *testing.T) {
+	fileStateService := services.NewFileStateService()
+	processor := services.NewWorkflowProcessor(
+		services.NewPatternMatcher(),
+		services.NewPathTransformer(),
+		fileStateService,
+		nil,
+		&mockMessageTemplater{},
+	)
+
+	workflow := createTestWorkflow("test-workflow", []types.Transformation{})
+
+	changedFiles := []types.ChangedFile{
+		{Path: "src/main.go", Status: "removed"},
+	}
+
+	err := processor.ProcessWorkflow(context.Background(), workflow, changedFiles, 1, "abc123")
+	require.NoError(t, err)
+
+	deprecated := fileStateService.GetFilesToDeprecate()
+	assert.Empty(t, deprecated, "expected no files to be processed with no transformations")
+}
+
+// ============================================================================
+// Tests for Invalid Patterns
+// ============================================================================
+
+func TestWorkflowProcessor_InvalidExcludePattern(t *testing.T) {
+	fileStateService := services.NewFileStateService()
+	processor := services.NewWorkflowProcessor(
+		services.NewPatternMatcher(),
+		services.NewPathTransformer(),
+		fileStateService,
+		nil,
+		&mockMessageTemplater{},
+	)
+
+	workflow := types.Workflow{
+		Name: "test-workflow",
+		Source: types.Source{
+			Repo:   "test-org/source-repo",
+			Branch: "main",
+		},
+		Destination: types.Destination{
+			Repo:   "test-org/dest-repo",
+			Branch: "main",
+		},
+		Transformations: []types.Transformation{
+			createMoveTransformation("src", "dest"),
+		},
+		// Invalid glob pattern - should be handled gracefully
+		Exclude: []string{"[invalid"},
+	}
+
+	changedFiles := []types.ChangedFile{
+		{Path: "src/main.go", Status: "removed"},
+	}
+
+	// Should not error, just log warning and continue
+	err := processor.ProcessWorkflow(context.Background(), workflow, changedFiles, 1, "abc123")
+	require.NoError(t, err)
+
+	// File should still be processed since invalid pattern is skipped
+	deprecated := fileStateService.GetFilesToDeprecate()
+	assert.NotEmpty(t, deprecated, "expected file to be processed despite invalid exclude pattern")
+}
+
+// ============================================================================
+// Tests for Deprecation Config
+// ============================================================================
+
+func TestWorkflowProcessor_CustomDeprecationFile(t *testing.T) {
+	fileStateService := services.NewFileStateService()
+	processor := services.NewWorkflowProcessor(
+		services.NewPatternMatcher(),
+		services.NewPathTransformer(),
+		fileStateService,
+		nil,
+		&mockMessageTemplater{},
+	)
+
+	workflow := types.Workflow{
+		Name: "test-workflow",
+		Source: types.Source{
+			Repo:   "test-org/source-repo",
+			Branch: "main",
+		},
+		Destination: types.Destination{
+			Repo:   "test-org/dest-repo",
+			Branch: "main",
+		},
+		Transformations: []types.Transformation{
+			createMoveTransformation("src", "dest"),
+		},
+		DeprecationCheck: &types.DeprecationConfig{
+			File: "custom_deprecation.json",
+		},
+	}
+
+	changedFiles := []types.ChangedFile{
+		{Path: "src/main.go", Status: "removed"},
+	}
+
+	err := processor.ProcessWorkflow(context.Background(), workflow, changedFiles, 1, "abc123")
+	require.NoError(t, err)
+
+	deprecated := fileStateService.GetFilesToDeprecate()
+	entries, exists := deprecated["custom_deprecation.json"]
+	assert.True(t, exists, "expected custom deprecation file to be used")
+	require.Len(t, entries, 1, "expected one entry in custom deprecation file")
+	assert.Equal(t, "dest/main.go", entries[0].FileName)
+}
+
+// ============================================================================
+// Tests for File Status Handling
+// ============================================================================
+
+func TestWorkflowProcessor_FileStatusHandling(t *testing.T) {
+	tests := []struct {
+		name             string
+		status           string
+		expectDeprecated bool
+	}{
+		{
+			name:             "removed file goes to deprecation",
+			status:           "removed",
+			expectDeprecated: true,
+		},
+		{
+			name:             "DELETED file goes to deprecation (GraphQL API format)",
+			status:           "DELETED",
+			expectDeprecated: true,
+		},
+		{
+			name:             "added file does not go to deprecation",
+			status:           "added",
+			expectDeprecated: false,
+		},
+		{
+			name:             "modified file does not go to deprecation",
+			status:           "modified",
+			expectDeprecated: false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			fileStateService := services.NewFileStateService()
+			processor := services.NewWorkflowProcessor(
+				services.NewPatternMatcher(),
+				services.NewPathTransformer(),
+				fileStateService,
+				nil,
+				&mockMessageTemplater{},
+			)
+
+			workflow := createTestWorkflow("test-workflow", []types.Transformation{
+				createMoveTransformation("src", "dest"),
+			})
+
+			changedFiles := []types.ChangedFile{
+				{Path: "src/main.go", Status: tt.status},
+			}
+
+			// Note: For non-removed files, this will try to call GitHub API
+			// which will fail, but we're testing the deprecation path
+			_ = processor.ProcessWorkflow(context.Background(), workflow, changedFiles, 1, "abc123")
+
+			deprecated := fileStateService.GetFilesToDeprecate()
+			if tt.expectDeprecated {
+				assert.NotEmpty(t, deprecated, "expected file to be in deprecation map")
+			} else {
+				// For non-removed files, they go to upload queue (which fails without GitHub)
+				// but should NOT be in deprecation map
+				assert.Empty(t, deprecated, "expected file NOT to be in deprecation map")
+			}
+		})
+	}
+}
+
+// ============================================================================
+// Tests for Path Transformation Edge Cases
+// ============================================================================
+
+func TestWorkflowProcessor_PathTransformationEdgeCases(t *testing.T) {
+	tests := []struct {
+		name       string
+		transform  types.Transformation
+		sourcePath string
+		wantMatch  bool
+	}{
+		{
+			name:       "move with trailing slash in from",
+			transform:  createMoveTransformation("src/", "dest/"),
+			sourcePath: "src/main.go",
+			wantMatch:  true,
+		},
+		{
+			name:       "move empty from does not match root file",
+			transform:  createMoveTransformation("", "dest"),
+			sourcePath: "main.go",
+			wantMatch:  false, // Empty prefix doesn't match in current implementation
+		},
+		{
+			name:       "glob single star does not match nested",
+			transform:  createGlobTransformation("src/*.go", "dest/${relative_path}"),
+			sourcePath: "src/pkg/main.go",
+			wantMatch:  false,
+		},
+		{
+			name:       "copy exact file match",
+			transform:  createCopyTransformation("README.md", "docs/README.md"),
+			sourcePath: "README.md",
+			wantMatch:  true,
+		},
+		{
+			name:       "copy does not match different file",
+			transform:  createCopyTransformation("README.md", "docs/README.md"),
+			sourcePath: "CHANGELOG.md",
+			wantMatch:  false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			fileStateService := services.NewFileStateService()
+			processor := services.NewWorkflowProcessor(
+				services.NewPatternMatcher(),
+				services.NewPathTransformer(),
+				fileStateService,
+				nil,
+				&mockMessageTemplater{},
+			)
+
+			workflow := createTestWorkflow("test-workflow", []types.Transformation{tt.transform})
+
+			changedFiles := []types.ChangedFile{
+				{Path: tt.sourcePath, Status: "removed"},
+			}
+
+			err := processor.ProcessWorkflow(context.Background(), workflow, changedFiles, 1, "abc123")
+			require.NoError(t, err)
+
+			deprecated := fileStateService.GetFilesToDeprecate()
+			if tt.wantMatch {
+				assert.NotEmpty(t, deprecated, "expected file to match transformation")
+			} else {
+				assert.Empty(t, deprecated, "expected file NOT to match transformation")
+			}
+		})
+	}
+}
diff --git a/testdata/.env.test b/testdata/.env.test
new file mode 100644
index 0000000..40a9066
--- /dev/null
+++ b/testdata/.env.test
@@ -0,0 +1,59 @@
+# Test environment configuration
+# Usage: cp testdata/.env.test .env.test && edit with your values
+
+# =============================================================================
+# REQUIRED - Fill these in
+# =============================================================================
+
+GITHUB_APP_ID=your-app-id
+INSTALLATION_ID=your-installation-id
+
+# Config repo points to your test source repo
+CONFIG_REPO_OWNER=cbullinger
+CONFIG_REPO_NAME=copier-app-source-test
+CONFIG_REPO_BRANCH=main
+
+# Main config file path in the source repo
+MAIN_CONFIG_FILE=.copier/main.yaml
+USE_MAIN_CONFIG=true
+
+# =============================================================================
+# SECRETS - Choose one method
+# =============================================================================
+
+# Option 1: Skip Secret Manager (easiest for local testing)
+SKIP_SECRET_MANAGER=true
+# Then set the private key directly (base64 encoded):
+# GITHUB_APP_PRIVATE_KEY_B64=your-base64-encoded-pem
+
+# Option 2: Use Secret Manager (if you have GCP access)
+# PEM_NAME=projects/YOUR_PROJECT/secrets/YOUR_SECRET/versions/latest
+
+# Webhook secret (must match what you set in GitHub)
+WEBHOOK_SECRET=your-webhook-secret
+
+# =============================================================================
+# TEST SETTINGS
+# =============================================================================
+
+# Dry run - process webhooks but don't make actual commits/PRs
+DRY_RUN=false
+
+# Disable cloud logging for local testing
+COPIER_DISABLE_CLOUD_LOGGING=true
+
+# Debug logging
+LOG_LEVEL=debug
+COPIER_DEBUG=true
+
+# Disable audit logging (no MongoDB needed)
+AUDIT_ENABLED=false
+
+# Server
+PORT=8080
+WEBSERVER_PATH=/webhook
+
+# Committer info for test PRs
+COMMITTER_NAME=Test Copier Bot
+COMMITTER_EMAIL=test-bot@example.com
+
diff --git a/test-payloads/README.md b/testdata/README.md
similarity index 60%
rename from test-payloads/README.md
rename to testdata/README.md
index 2f9e474..8497088 100644
--- a/test-payloads/README.md
+++ b/testdata/README.md
@@ -1,6 +1,56 @@
 # Test Payloads
 
-This directory contains example webhook payloads for testing the examples-copier application.
+Test files for local integration testing of the github-copier app.
+
+## Quick Start (Isolated Testing)
+
+```bash
+# 1. Copy and configure test environment
+cp testdata/.env.test .env.test
+# Edit .env.test with your GitHub App credentials
+
+# 2. Copy config to your test source repo (cbullinger/copier-app-source-test)
+# Upload testdata/source-repo-files/.copier/main.yaml to .copier/main.yaml
+
+# 3. Start the app with test config
+ENV_FILE=.env.test go run app.go
+
+# 4. In another terminal, start webhook tunnel
+smee --url https://smee.io/YOUR_CHANNEL --target http://localhost:8080/webhook
+
+# 5. Create a PR in your test source repo and merge it
+```
+
+## Directory Structure
+
+```
+testdata/
+├── .env.test                    # Test environment variables (copy to .env.test)
+├── source-repo-files/           # Files to copy to your test source repo
+│   └── .copier/
+│       └── main.yaml            # Workflow config for test repos
+├── test-pr-merged.json          # Sample webhook payload
+├── test-config.yaml             # Example config (reference only)
+└── example-pr-merged.json       # Generic example payload
+```
+
+## Test Repositories
+
+| Repo | Purpose |
+|------|---------|
+| `cbullinger/copier-app-source-test` | Source repo (receives PRs, triggers webhooks) |
+| `cbullinger/copier-app-dest-1` | Destination for Go examples |
+| `cbullinger/copier-app-dest-2` | Destination for Python examples |
+
+## Configured Workflows
+
+The test config (`source-repo-files/.copier/main.yaml`) defines:
+
+| Workflow | Source Pattern | Destination | Transform |
+|----------|---------------|-------------|-----------|
+| `test-go-to-dest1` | `examples/go/**` | `copier-app-dest-1` | `examples/go/` → `go-examples/` |
+| `test-python-to-dest2` | `examples/python/**` | `copier-app-dest-2` | `examples/python/` → `python-examples/` |
+| `test-docs-to-dest1` | `docs/**` | `copier-app-dest-1` | `docs/` → `documentation/` |
 
 ## Files
 
@@ -20,7 +70,7 @@ A complete example of a merged PR webhook payload with:
 go build -o test-webhook ./cmd/test-webhook
 
 # Send example payload
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 ```
 
 ### Option 2: Fetch Real PR Data
@@ -124,10 +174,10 @@ Test without making actual commits:
 
 ```bash
 # Start app in dry-run mode
-DRY_RUN=true ./examples-copier &
+DRY_RUN=true ./github-copier &
 
 # Send test webhook
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 
 # Check logs for pattern matching and transformations
 ```
@@ -164,7 +214,7 @@ After sending a test webhook:
 
 ### Test Case 1: New Go Examples
 ```bash
-./test-webhook -payload test-payloads/example-pr-merged.json
+./test-webhook -payload testdata/example-pr-merged.json
 ```
 Expected: Files copied to target repo with transformed paths
 
@@ -177,8 +227,8 @@ Expected: Real PR data fetched and processed
 
 ### Test Case 3: Dry-Run Validation
 ```bash
-DRY_RUN=true ./examples-copier &
-./test-webhook -payload test-payloads/example-pr-merged.json
+DRY_RUN=true ./github-copier &
+./test-webhook -payload testdata/example-pr-merged.json
 ```
 Expected: Processing logged but no commits made
 
diff --git a/test-payloads/example-pr-merged.json b/testdata/example-pr-merged.json
similarity index 100%
rename from test-payloads/example-pr-merged.json
rename to testdata/example-pr-merged.json
diff --git a/testdata/source-repo-files/.copier/main.yaml b/testdata/source-repo-files/.copier/main.yaml
new file mode 100644
index 0000000..fab2660
--- /dev/null
+++ b/testdata/source-repo-files/.copier/main.yaml
@@ -0,0 +1,61 @@
+# Main config for test source repo: cbullinger/copier-app-source-test
+# Copy this file to .copier/main.yaml in your source repo
+
+defaults:
+  commit_strategy:
+    type: "pull_request"
+    auto_merge: false
+
+workflow_configs:
+  - source: "inline"
+    workflows:
+      # Workflow 1: Copy Go files to dest-1
+      - name: "test-go-to-dest1"
+        source:
+          patterns:
+            - "examples/go/**"
+        destination:
+          repo: "cbullinger/copier-app-dest-1"
+          branch: "main"
+        transformations:
+          - move:
+              from: "examples/go/"
+              to: "go-examples/"
+        commit_strategy:
+          type: "pull_request"
+          pr_title: "[Test] Sync Go examples"
+          auto_merge: false
+
+      # Workflow 2: Copy Python files to dest-2
+      - name: "test-python-to-dest2"
+        source:
+          patterns:
+            - "examples/python/**"
+        destination:
+          repo: "cbullinger/copier-app-dest-2"
+          branch: "main"
+        transformations:
+          - move:
+              from: "examples/python/"
+              to: "python-examples/"
+        commit_strategy:
+          type: "pull_request"
+          pr_title: "[Test] Sync Python examples"
+          auto_merge: false
+
+      # Workflow 3: Copy shared docs to both destinations
+      - name: "test-docs-to-dest1"
+        source:
+          patterns:
+            - "docs/**"
+        destination:
+          repo: "cbullinger/copier-app-dest-1"
+          branch: "main"
+        transformations:
+          - move:
+              from: "docs/"
+              to: "documentation/"
+        commit_strategy:
+          type: "direct"
+          message: "Sync docs from source"
+
diff --git a/testdata/test-config.yaml b/testdata/test-config.yaml
new file mode 100644
index 0000000..181c191
--- /dev/null
+++ b/testdata/test-config.yaml
@@ -0,0 +1,66 @@
+# Test configuration for local integration testing
+# Source: cbullinger/copier-app-source-test
+# Destinations: cbullinger/copier-app-dest-1, cbullinger/copier-app-dest-2
+
+workflows:
+  # Workflow 1: Copy Go files to dest-1
+  - name: "test-go-to-dest1"
+    source:
+      repo: "cbullinger/copier-app-source-test"
+      branch: "main"
+      patterns:
+        - type: glob
+          pattern: "examples/go/**"
+    destination:
+      repo: "cbullinger/copier-app-dest-1"
+      branch: "main"
+    transformations:
+      - type: move
+        from: "examples/go/"
+        to: "go-examples/"
+    commit:
+      strategy: pr
+      message: "Sync Go examples from source"
+      pr_title: "[Test] Sync Go examples"
+      auto_merge: false
+
+  # Workflow 2: Copy Python files to dest-2
+  - name: "test-python-to-dest2"
+    source:
+      repo: "cbullinger/copier-app-source-test"
+      branch: "main"
+      patterns:
+        - type: glob
+          pattern: "examples/python/**"
+    destination:
+      repo: "cbullinger/copier-app-dest-2"
+      branch: "main"
+    transformations:
+      - type: move
+        from: "examples/python/"
+        to: "python-examples/"
+    commit:
+      strategy: pr
+      message: "Sync Python examples from source"
+      pr_title: "[Test] Sync Python examples"
+      auto_merge: false
+
+  # Workflow 3: Copy docs to both destinations
+  - name: "test-docs-to-dest1"
+    source:
+      repo: "cbullinger/copier-app-source-test"
+      branch: "main"
+      patterns:
+        - type: glob
+          pattern: "docs/**"
+    destination:
+      repo: "cbullinger/copier-app-dest-1"
+      branch: "main"
+    transformations:
+      - type: move
+        from: "docs/"
+        to: "documentation/"
+    commit:
+      strategy: direct
+      message: "Sync docs from source"
+
diff --git a/testdata/test-pr-merged.json b/testdata/test-pr-merged.json
new file mode 100644
index 0000000..d8a799b
--- /dev/null
+++ b/testdata/test-pr-merged.json
@@ -0,0 +1,67 @@
+{
+  "action": "closed",
+  "number": 1,
+  "pull_request": {
+    "number": 1,
+    "state": "closed",
+    "merged": true,
+    "merge_commit_sha": "test123abc456def",
+    "title": "Test PR for integration testing",
+    "head": {
+      "ref": "test-branch",
+      "sha": "abc123test",
+      "repo": {
+        "name": "copier-app-source-test",
+        "full_name": "cbullinger/copier-app-source-test"
+      }
+    },
+    "base": {
+      "ref": "main",
+      "repo": {
+        "name": "copier-app-source-test",
+        "full_name": "cbullinger/copier-app-source-test"
+      }
+    }
+  },
+  "repository": {
+    "name": "copier-app-source-test",
+    "full_name": "cbullinger/copier-app-source-test",
+    "owner": {
+      "login": "cbullinger"
+    }
+  },
+  "installation": {
+    "id": 12345678
+  },
+  "files": [
+    {
+      "filename": "examples/go/main.go",
+      "status": "added",
+      "additions": 20,
+      "deletions": 0,
+      "changes": 20
+    },
+    {
+      "filename": "examples/go/utils/helper.go",
+      "status": "added",
+      "additions": 15,
+      "deletions": 0,
+      "changes": 15
+    },
+    {
+      "filename": "examples/python/app.py",
+      "status": "added",
+      "additions": 30,
+      "deletions": 0,
+      "changes": 30
+    },
+    {
+      "filename": "docs/README.md",
+      "status": "modified",
+      "additions": 5,
+      "deletions": 2,
+      "changes": 7
+    }
+  ]
+}
+
diff --git a/tests/utils.go b/tests/utils.go
index ddf2b33..4bc2ff2 100644
--- a/tests/utils.go
+++ b/tests/utils.go
@@ -10,9 +10,9 @@ import (
 
 	"github.com/jarcoal/httpmock"
 
-	"github.com/mongodb/code-example-tooling/code-copier/configs"
-	"github.com/mongodb/code-example-tooling/code-copier/services"
-	"github.com/mongodb/code-example-tooling/code-copier/types"
+	"github.com/grove-platform/github-copier/configs"
+	"github.com/grove-platform/github-copier/services"
+	"github.com/grove-platform/github-copier/types"
 )
 
 //