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.claude/commands/add-to-todos.md

@@ -0,0 +1,56 @@
+---
+description: Add todo item to TO-DOS.md with context from conversation
+argument-hint: <todo-description> (optional - infers from conversation if omitted)
+allowed-tools:
+  - Read
+  - Edit
+  - Write
+---
+
+# Add Todo Item
+
+## Context
+
+- Current timestamp: !`date "+%Y-%m-%d %H:%M"`
+
+## Instructions
+
+1. Read TO-DOS.md in the working directory (create with Write tool if it doesn't exist)
+
+2. Check for duplicates:
+   - Extract key concept/action from the new todo
+   - Search existing todos for similar titles or overlapping scope
+   - If found, ask user: "A similar todo already exists: [title]. Would you like to:\n\n1. Skip adding (keep existing)\n2. Replace existing with new version\n3. Add anyway as separate item\n\nReply with the number of your choice."
+   - Wait for user response before proceeding
+
+3. Extract todo content:
+   - **With $ARGUMENTS**: Use as the focus/title for the todo and context heading
+   - **Without $ARGUMENTS**: Analyze recent conversation to extract:
+     - Specific problem or task discussed
+     - Relevant file paths that need attention
+     - Technical details (line numbers, error messages, conflicting specifications)
+     - Root cause if identified
+
+4. Append new section to bottom of file:
+   - **Heading**: `## Brief Context Title - YYYY-MM-DD HH:MM` (3-8 word title, current timestamp)
+   - **Todo format**: `- **[Action verb] [Component]** - [Brief description]. **Problem:** [What's wrong/why needed]. **Files:** [Comma-separated paths with line numbers]. **Solution:** [Approach hints or constraints, if applicable].`
+   - **Required fields**: Problem and Files (with line numbers like `path/to/file.ts:123-145`)
+   - **Optional field**: Solution
+   - Make each section self-contained for future Claude to understand weeks later
+   - Use simple list items (not checkboxes) - todos are removed when work begins
+
+5. Confirm and offer to continue with original work:
+   - Identify what the user was working on before `/add-to-todos` was called
+   - Confirm the todo was saved: "✓ Saved to todos."
+   - Ask if they want to continue with the original work: "Would you like to continue with [original task]?"
+   - Wait for user response
+
+## Format Example
+
+```markdown
+## Add Todo Command Improvements - 2025-11-15 14:23
+
+- **Add structured format to add-to-todos** - Standardize todo entries with Problem/Files/Solution pattern. **Problem:** Current todos lack consistent structure, making it hard for Claude to have enough context when revisiting tasks later. **Files:** `commands/add-to-todos.md:22-29`. **Solution:** Use inline bold labels with required Problem and Files fields, optional Solution field.
+
+- **Create check-todos command** - Build companion command to list and select todos. **Problem:** Need workflow to review outstanding todos and load context for selected item. **Files:** `commands/check-todos.md` (new), `TO-DOS.md` (reads from). **Solution:** Parse markdown list, display numbered list, accept selection to load full context and remove item.
+```

.claude/commands/audit-skill.md

@@ -0,0 +1,24 @@
+---
+description: Audit skill for YAML compliance, pure XML structure, progressive disclosure, and best practices
+argument-hint: <skill-path>
+---
+
+<objective>
+Invoke the skill-auditor subagent to audit the skill at $ARGUMENTS for compliance with Agent Skills best practices.
+
+This ensures skills follow proper structure (pure XML, required tags, progressive disclosure) and effectiveness patterns.
+</objective>
+
+<process>
+1. Invoke skill-auditor subagent
+2. Pass skill path: $ARGUMENTS
+3. Subagent will read updated best practices (including pure XML structure requirements)
+4. Subagent evaluates XML structure quality, required/conditional tags, anti-patterns
+5. Review detailed findings with file:line locations, compliance scores, and recommendations
+</process>
+
+<success_criteria>
+- Subagent invoked successfully
+- Arguments passed correctly to subagent
+- Audit includes XML structure evaluation
+</success_criteria>

.claude/commands/audit-slash-command.md

@@ -0,0 +1,22 @@
+---
+description: Audit slash command file for YAML, arguments, dynamic context, tool restrictions, and content quality
+argument-hint: <command-path>
+---
+
+<objective>
+Invoke the slash-command-auditor subagent to audit the slash command at $ARGUMENTS for compliance with best practices.
+
+This ensures commands follow security, clarity, and effectiveness standards.
+</objective>
+
+<process>
+1. Invoke slash-command-auditor subagent
+2. Pass command path: $ARGUMENTS
+3. Subagent will read best practices and evaluate the command
+4. Review detailed findings with file:line locations, compliance scores, and recommendations
+</process>
+
+<success_criteria>
+- Subagent invoked successfully
+- Arguments passed correctly to subagent
+</success_criteria>

.claude/commands/audit-subagent.md

@@ -0,0 +1,22 @@
+---
+description: Audit subagent configuration for role definition, prompt quality, tool selection, XML structure compliance, and effectiveness
+argument-hint: <subagent-path>
+---
+
+<objective>
+Invoke the subagent-auditor subagent to audit the subagent at $ARGUMENTS for compliance with best practices, including pure XML structure standards.
+
+This ensures subagents follow proper structure, configuration, pure XML formatting, and implementation patterns.
+</objective>
+
+<process>
+1. Invoke subagent-auditor subagent
+2. Pass subagent path: $ARGUMENTS
+3. Subagent will read best practices and evaluate the configuration
+4. Review detailed findings with file:line locations, compliance scores, and recommendations
+</process>
+
+<success_criteria>
+- Subagent invoked successfully
+- Arguments passed correctly to subagent
+</success_criteria>

.claude/commands/automation/README.md

@@ -4,6 +4,11 @@ Commands for automation operations in Claude Flow.
 
 ## Available Commands
 
+- [ai-pipeline](./ai-pipeline.md) - **NEW**: Autonomous AI/ML research-to-implementation pipeline
 - [auto-agent](./auto-agent.md)
 - [smart-spawn](./smart-spawn.md)
 - [workflow-select](./workflow-select.md)
+- [research-plan-only](./research-plan-only.md)
+- [session-memory](./session-memory.md)
+- [self-healing](./self-healing.md)
+- [smart-agents](./smart-agents.md)