Fix documentation discrepancies: payload threshold and internal directories

- Update README.md default payload size threshold from 1024 to 10240 bytes (3 locations)
- Add missing 9 internal directories to CONTRIBUTING.md project structure
- Add missing 7 internal directories to AGENTS.md project structure
- All 16 internal directories now documented in alphabetical order

Co-authored-by: lpcox <15877973+lpcox@users.noreply.github.com>

Author: Claude

AGENTS.md

@@ -21,17 +21,24 @@ Quick reference for AI agents working with MCP Gateway (Go-based MCP proxy serve
 
 ## Project Structure
 
+- `internal/auth/` - Authentication header parsing and middleware
 - `internal/cmd/` - CLI (Cobra)
 - `internal/config/` - Config parsing (TOML/JSON) with validation
   - `validation.go` - Variable expansion and fail-fast validation
   - `validation_test.go` - 21 comprehensive validation tests
-- `internal/server/` - HTTP server (routed/unified modes)
-- `internal/mcp/` - MCP protocol types with enhanced error logging
-- `internal/launcher/` - Backend process management
+- `internal/difc/` - Data Information Flow Control
+- `internal/envutil/` - Environment variable utilities
 - `internal/guard/` - Security guards (NoopGuard active)
-- `internal/auth/` - Authentication header parsing and middleware
+- `internal/launcher/` - Backend process management
 - `internal/logger/` - Debug logging framework (micro logger)
+- `internal/mcp/` - MCP protocol types with enhanced error logging
+- `internal/middleware/` - HTTP middleware (jq schema processing)
+- `internal/server/` - HTTP server (routed/unified modes)
+- `internal/sys/` - System utilities
+- `internal/testutil/` - Test utilities and helpers
 - `internal/timeutil/` - Time formatting utilities
+- `internal/tty/` - Terminal detection utilities
+- `internal/version/` - Version management
 
 ## Key Tech
 

CONTRIBUTING.md

@@ -211,26 +211,42 @@ awmg/
 ├── Dockerfile                 # Container image
 ├── Makefile                   # Build automation
 └── internal/
+    ├── auth/                  # Authentication header parsing and middleware
     ├── cmd/                   # CLI commands (cobra)
     ├── config/                # Configuration loading (TOML/JSON)
+    ├── difc/                  # Data Information Flow Control
+    ├── envutil/               # Environment variable utilities
+    ├── guard/                 # Security guards (NoopGuard active)
     ├── launcher/              # Backend server management
+    ├── logger/                # Debug logging framework
     ├── mcp/                   # MCP protocol types & connection
+    ├── middleware/            # HTTP middleware (jq schema processing)
     ├── server/                # HTTP server (routed/unified modes)
-    ├── guard/                 # Security guards (NoopGuard active)
-    ├── logger/                # Debug logging framework
+    ├── sys/                   # System utilities
+    ├── testutil/              # Test utilities and helpers
     ├── timeutil/              # Time formatting utilities
-    └── tty/                   # Terminal detection utilities
+    ├── tty/                   # Terminal detection utilities
+    └── version/               # Version management
 ```
 
 ### Key Directories
 
+- **`internal/auth/`** - Authentication header parsing and middleware
 - **`internal/cmd/`** - CLI implementation using Cobra framework
 - **`internal/config/`** - Configuration parsing for TOML and JSON formats
-- **`internal/server/`** - HTTP server with routed and unified modes
-- **`internal/mcp/`** - MCP protocol types and JSON-RPC handling
-- **`internal/launcher/`** - Backend process management (Docker, stdio)
+- **`internal/difc/`** - Data Information Flow Control
+- **`internal/envutil/`** - Environment variable utilities
 - **`internal/guard/`** - Guard framework for resource labeling
+- **`internal/launcher/`** - Backend process management (Docker, stdio)
 - **`internal/logger/`** - Micro logger for debug output
+- **`internal/mcp/`** - MCP protocol types and JSON-RPC handling
+- **`internal/middleware/`** - HTTP middleware (jq schema processing)
+- **`internal/server/`** - HTTP server with routed and unified modes
+- **`internal/sys/`** - System utilities
+- **`internal/testutil/`** - Test utilities and helpers
+- **`internal/timeutil/`** - Time formatting utilities
+- **`internal/tty/`** - Terminal detection utilities
+- **`internal/version/`** - Version management
 
 ## Coding Conventions
 

README.md

@@ -202,7 +202,7 @@ See **[Configuration Specification](https://github.com/github/gh-aw/blob/main/do
 
 **Configuration Alternatives**:
 - **`payloadSizeThreshold`** is not supported in JSON stdin format. Use:
-  - CLI flag: `--payload-size-threshold <bytes>` (default: 1024)
+  - CLI flag: `--payload-size-threshold <bytes>` (default: 10240)
   - Environment variable: `MCP_GATEWAY_PAYLOAD_SIZE_THRESHOLD=<bytes>`
   - Payloads **larger** than this threshold are stored to disk and return metadata
   - Payloads **smaller than or equal** to this threshold are returned inline
@@ -278,7 +278,7 @@ Flags:
   -l, --listen string                HTTP server listen address (default "127.0.0.1:3000")
       --log-dir string               Directory for log files (falls back to stdout if directory cannot be created) (default "/tmp/gh-aw/mcp-logs")
       --payload-dir string           Directory for storing large payload files (segmented by session ID) (default "/tmp/jq-payloads")
-      --payload-size-threshold int   Size threshold (in bytes) for storing payloads to disk. Payloads larger than this are stored, smaller ones returned inline (default 1024)
+      --payload-size-threshold int   Size threshold (in bytes) for storing payloads to disk. Payloads larger than this are stored, smaller ones returned inline (default 10240)
       --routed                       Run in routed mode (each backend at /mcp/<server>)
       --sequential-launch   Launch MCP servers sequentially during startup (parallel launch is default)
       --unified             Run in unified mode (all backends at /mcp)
@@ -316,7 +316,7 @@ When running locally (`run.sh`), these variables are optional (warnings shown if
 | `MODE` | Gateway mode flag | `--routed` |
 | `MCP_GATEWAY_LOG_DIR` | Log file directory (sets default for `--log-dir` flag) | `/tmp/gh-aw/mcp-logs` |
 | `MCP_GATEWAY_PAYLOAD_DIR` | Large payload storage directory (sets default for `--payload-dir` flag) | `/tmp/jq-payloads` |
-| `MCP_GATEWAY_PAYLOAD_SIZE_THRESHOLD` | Size threshold in bytes for payload storage (sets default for `--payload-size-threshold` flag) | `1024` |
+| `MCP_GATEWAY_PAYLOAD_SIZE_THRESHOLD` | Size threshold in bytes for payload storage (sets default for `--payload-size-threshold` flag) | `10240` |
 
 ### Docker Configuration