codexkit 1.0.0

package/.codex/skills/index-knowledge/SKILL.md

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+---
+name: index-knowledge
+description: Generate hierarchical AGENTS.md knowledge base for a codebase. Creates root + complexity-scored subdirectory documentation.
+version: 1.0.0
+tags: [documentation, workflow]
+dependencies: []
+---
+
+# index-knowledge
+
+## When to Use
+
+- When you need to generate or update hierarchical AGENTS.md documentation for a codebase.
+
+## When NOT to Use
+
+- When only a single small directory needs a manual note instead of a full knowledge hierarchy.
+
+
+## Usage
+
+```
+/index-knowledge                  # Update mode (default)
+/index-knowledge --create-new     # Delete all → regenerate from scratch
+/index-knowledge --max-depth=2    # Limit directory depth (default: 5)
+```
+
+## Load Skills
+
+```typescript
+skill({ name: "memory-system" }); // Search for existing patterns
+skill({ name: "deep-research" }); // For thorough LSP exploration
+```
+
+## Check Memory First
+
+```typescript
+memory_search({ query: "AGENTS.md conventions patterns", limit: 3 });
+```
+
+---
+
+## Workflow (High-Level)
+
+1. **Discovery + Analysis** (concurrent)
+   - Launch parallel explore agents (multiple Task calls in one message)
+   - Main session: bash structure + LSP codemap + read existing AGENTS.md
+2. **Score & Decide** - Determine AGENTS.md locations from merged findings
+3. **Generate** - Root first, then subdirs in parallel
+4. **Review** - Deduplicate, trim, validate
+
+<critical>
+**TodoWrite ALL phases. Mark in_progress → completed in real-time.**
+  
+```typescript
+todowrite({ todos: [
+  { id: "discovery", content: "Fire explore agents + LSP codemap + read existing", status: "pending", priority: "high" },
+  { id: "scoring", content: "Score directories, determine locations", status: "pending", priority: "high" },
+  { id: "generate", content: "Generate AGENTS.md files (root + subdirs)", status: "pending", priority: "high" },
+  { id: "review", content: "Deduplicate, validate, trim", status: "pending", priority: "medium" }
+]});
+```
+</critical>
+
+---
+
+## Phase 1: Discovery + Analysis (Concurrent)
+
+**Mark "discovery" as in_progress.**
+
+### Launch Parallel Explore Agents
+
+Multiple Task calls in a single message execute in parallel. Results return directly.
+
+```
+// All Task calls in ONE message = parallel execution
+
+Task(
+  description="project structure",
+  subagent_type="explore",
+  prompt="Project structure: PREDICT standard patterns for detected language → REPORT deviations only"
+)
+
+Task(
+  description="entry points",
+  subagent_type="explore",
+  prompt="Entry points: FIND main files → REPORT non-standard organization"
+)
+
+Task(
+  description="conventions",
+  subagent_type="explore",
+  prompt="Conventions: FIND config files (.eslintrc, pyproject.toml, .editorconfig) → REPORT project-specific rules"
+)
+
+Task(
+  description="anti-patterns",
+  subagent_type="explore",
+  prompt="Anti-patterns: FIND 'DO NOT', 'NEVER', 'ALWAYS', 'DEPRECATED' comments → LIST forbidden patterns"
+)
+
+Task(
+  description="build/ci",
+  subagent_type="explore",
+  prompt="Build/CI: FIND .github/workflows, Makefile → REPORT non-standard patterns"
+)
+
+Task(
+  description="test patterns",
+  subagent_type="explore",
+  prompt="Test patterns: FIND test configs, test structure → REPORT unique conventions"
+)
+```
+
+<dynamic-agents>
+**DYNAMIC AGENT SPAWNING**: After bash analysis, spawn ADDITIONAL explore agents based on project scale:
+
+| Factor                       | Threshold | Additional Agents          |
+| ---------------------------- | --------- | -------------------------- |
+| **Total files**              | >100      | +1 per 100 files           |
+| **Total lines**              | >10k      | +1 per 10k lines           |
+| **Directory depth**          | ≥4        | +2 for deep exploration    |
+| **Large files (>500 lines)** | >10 files | +1 for complexity hotspots |
+| **Monorepo**                 | detected  | +1 per package/workspace   |
+| **Multiple languages**       | >1        | +1 per language            |
+
+```bash
+# Measure project scale first
+total_files=$(find . -type f -not -path '*/node_modules/*' -not -path '*/.git/*' | wc -l)
+total_lines=$(find . -type f \( -name "*.ts" -o -name "*.py" -o -name "*.go" \) -not -path '*/node_modules/*' -exec wc -l {} + 2>/dev/null | tail -1 | awk '{print $1}')
+large_files=$(find . -type f \( -name "*.ts" -o -name "*.py" \) -not -path '*/node_modules/*' -exec wc -l {} + 2>/dev/null | awk '$1 > 500 {count++} END {print count+0}')
+max_depth=$(find . -type d -not -path '*/node_modules/*' -not -path '*/.git/*' | awk -F/ '{print NF}' | sort -rn | head -1)
+```
+
+Example spawning (all in ONE message for parallel execution):
+
+```
+// 500 files, 50k lines, depth 6, 15 large files → spawn additional agents
+Task(
+  description="large files",
+  subagent_type="explore",
+  prompt="Large file analysis: FIND files >500 lines, REPORT complexity hotspots"
+)
+
+Task(
+  description="deep modules",
+  subagent_type="explore",
+  prompt="Deep modules at depth 4+: FIND hidden patterns, internal conventions"
+)
+
+Task(
+  description="cross-cutting",
+  subagent_type="explore",
+  prompt="Cross-cutting concerns: FIND shared utilities across directories"
+)
+// ... more based on calculation
+```
+
+</dynamic-agents>
+
+### Main Session: Concurrent Analysis
+
+**While Task agents execute**, main session does:
+
+#### 1. Bash Structural Analysis
+
+```bash
+# Directory depth + file counts
+find . -type d -not -path '*/\.*' -not -path '*/node_modules/*' -not -path '*/venv/*' -not -path '*/dist/*' -not -path '*/build/*' | awk -F/ '{print NF-1}' | sort -n | uniq -c
+
+# Files per directory (top 30)
+find . -type f -not -path '*/\.*' -not -path '*/node_modules/*' | sed 's|/[^/]*$||' | sort | uniq -c | sort -rn | head -30
+
+# Code concentration by extension
+find . -type f \( -name "*.py" -o -name "*.ts" -o -name "*.tsx" -o -name "*.js" -o -name "*.go" -o -name "*.rs" \) -not -path '*/node_modules/*' | sed 's|/[^/]*$||' | sort | uniq -c | sort -rn | head -20
+
+# Existing AGENTS.md / CLAUDE.md
+find . -type f \( -name "AGENTS.md" -o -name "CLAUDE.md" \) -not -path '*/node_modules/*' 2>/dev/null
+```
+
+#### 2. Read Existing AGENTS.md
+
+```
+For each existing file found:
+  Read(filePath=file)
+  Extract: key insights, conventions, anti-patterns
+  Store in EXISTING_AGENTS map
+```
+
+If `--create-new`: Read all existing first (preserve context) → then delete all → regenerate.
+
+#### 3. LSP Codemap (if available)
+
+```
+lsp_servers()  # Check availability
+
+# Entry points (parallel)
+lsp_document_symbols(filePath="src/index.ts")
+lsp_document_symbols(filePath="main.py")
+
+# Key symbols (parallel)
+lsp_workspace_symbols(filePath=".", query="class")
+lsp_workspace_symbols(filePath=".", query="interface")
+lsp_workspace_symbols(filePath=".", query="function")
+
+# Centrality for top exports
+lsp_find_references(filePath="...", line=X, character=Y)
+```
+
+**LSP Fallback**: If unavailable, rely on explore agents + AST-grep.
+
+**Merge: bash + LSP + existing + Task agent results. Mark "discovery" as completed.**
+
+---
+
+## Phase 2: Scoring & Location Decision
+
+**Mark "scoring" as in_progress.**
+
+### Scoring Matrix
+
+| Factor               | Weight | High Threshold           | Source  |
+| -------------------- | ------ | ------------------------ | ------- |
+| File count           | 3x     | >20                      | bash    |
+| Subdir count         | 2x     | >5                       | bash    |
+| Code ratio           | 2x     | >70%                     | bash    |
+| Unique patterns      | 1x     | Has own config           | explore |
+| Module boundary      | 2x     | Has index.ts/**init**.py | bash    |
+| Symbol density       | 2x     | >30 symbols              | LSP     |
+| Export count         | 2x     | >10 exports              | LSP     |
+| Reference centrality | 3x     | >20 refs                 | LSP     |
+
+### Decision Rules
+
+| Score        | Action                    |
+| ------------ | ------------------------- |
+| **Root (.)** | ALWAYS create             |
+| **>15**      | Create AGENTS.md          |
+| **8-15**     | Create if distinct domain |
+| **<8**       | Skip (parent covers)      |
+
+### Output
+
+```
+AGENTS_LOCATIONS = [
+  { path: ".", type: "root" },
+  { path: "src/hooks", score: 18, reason: "high complexity" },
+  { path: "src/api", score: 12, reason: "distinct domain" }
+]
+```
+
+**Mark "scoring" as completed.**
+
+---
+
+## Phase 3: Generate AGENTS.md
+
+**Mark "generate" as in_progress.**
+
+### Root AGENTS.md (Full Treatment)
+
+```markdown
+# PROJECT KNOWLEDGE BASE
+
+**Generated:** {TIMESTAMP}
+**Commit:** {SHORT_SHA}
+**Branch:** {BRANCH}
+
+## OVERVIEW
+
+{1-2 sentences: what + core stack}
+
+## STRUCTURE
+
+\`\`\`
+{root}/
+├── {dir}/ # {non-obvious purpose only}
+└── {entry}
+\`\`\`
+
+## WHERE TO LOOK
+
+| Task | Location | Notes |
+| ---- | -------- | ----- |
+
+## CODE MAP
+
+{From LSP - skip if unavailable or project <10 files}
+
+| Symbol | Type | Location | Refs | Role |
+
+## CONVENTIONS
+
+{ONLY deviations from standard}
+
+## ANTI-PATTERNS (THIS PROJECT)
+
+{Explicitly forbidden here}
+
+## UNIQUE STYLES
+
+{Project-specific}
+
+## COMMANDS
+
+\`\`\`bash
+{dev/test/build}
+\`\`\`
+
+## NOTES
+
+{Gotchas}
+```
+
+**Quality gates**: 50-150 lines, no generic advice, no obvious info.
+
+### Subdirectory AGENTS.md (Parallel)
+
+Launch general agents for each location in ONE message (parallel execution):
+
+```
+// All in single message = parallel
+Task(
+  description="AGENTS.md for src/hooks",
+  subagent_type="general",
+  prompt="Generate AGENTS.md for: src/hooks
+    - Reason: high complexity
+    - 30-80 lines max
+    - NEVER repeat parent content
+    - Sections: OVERVIEW (1 line), STRUCTURE (if >5 subdirs), WHERE TO LOOK, CONVENTIONS (if different), ANTI-PATTERNS
+    - Write directly to src/hooks/AGENTS.md"
+)
+
+Task(
+  description="AGENTS.md for src/api",
+  subagent_type="general",
+  prompt="Generate AGENTS.md for: src/api
+    - Reason: distinct domain
+    - 30-80 lines max
+    - NEVER repeat parent content
+    - Sections: OVERVIEW (1 line), STRUCTURE (if >5 subdirs), WHERE TO LOOK, CONVENTIONS (if different), ANTI-PATTERNS
+    - Write directly to src/api/AGENTS.md"
+)
+// ... one Task per AGENTS_LOCATIONS entry
+```
+
+**Results return directly. Mark "generate" as completed.**
+
+---
+
+## Phase 4: Review & Deduplicate
+
+**Mark "review" as in_progress.**
+
+For each generated file:
+
+- Remove generic advice
+- Remove parent duplicates
+- Trim to size limits
+- Verify telegraphic style
+
+**Mark "review" as completed.**
+
+---
+
+## Final Report
+
+```
+=== index-knowledge Complete ===
+
+Mode: {update | create-new}
+
+Files:
+  ✓ ./AGENTS.md (root, {N} lines)
+  ✓ ./src/hooks/AGENTS.md ({N} lines)
+
+Dirs Analyzed: {N}
+AGENTS.md Created: {N}
+AGENTS.md Updated: {N}
+
+Hierarchy:
+  ./AGENTS.md
+  └── src/hooks/AGENTS.md
+```
+
+---
+
+## Anti-Patterns
+
+- **Static agent count**: MUST vary agents based on project size/depth
+- **Sequential execution**: MUST parallel (multiple Task calls in one message)
+- **Ignoring existing**: ALWAYS read existing first, even with --create-new
+- **Over-documenting**: Not every dir needs AGENTS.md
+- **Redundancy**: Child never repeats parent
+- **Generic content**: Remove anything that applies to ALL projects
+- **Verbose style**: Telegraphic or die
+- **Skipping memory**: ALWAYS search memory for existing patterns before starting
+
+---
+
+## Record Findings
+
+After completion, save significant discoveries:
+
+```typescript
+observation({
+  type: "pattern",
+  title: "AGENTS.md patterns for [project]",
+  narrative: "[Key conventions, anti-patterns, structure decisions]",
+  concepts: "AGENTS.md, documentation, codebase, knowledge",
+  confidence: "high",
+});
+```

package/.codex/skills/jira/SKILL.md

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+---
+name: jira
+description: Jira and Confluence integration via official Atlassian MCP. Search issues, create tickets, update status, and access Confluence docs. Uses OAuth 2.1 authorization with Rovo Search.
+version: 1.0.0
+tags: [integration, mcp, workflow]
+dependencies: []
+---
+
+# Jira & Confluence Integration (MCP)
+
+## When to Use
+
+- When you need to search or update Jira/Confluence content via Atlassian MCP.
+
+## When NOT to Use
+
+- When the project does not use Atlassian Cloud or MCP access is unavailable.
+
+
+## Key Features
+
+- **OAuth 2.1 Authorization** - Secure browser-based authentication
+- **Rovo Search** - Unified search across Jira and Confluence
+- **Real-time Data** - Direct connection to Atlassian Cloud
+- **Permission-aware** - Respects existing user access controls
+
+## Available Tools
+
+### Universal Search (Recommended)
+
+- `search` - **Rovo Search** - Search Jira and Confluence content (use this by default)
+- `fetch` - Get details by ARI (Atlassian Resource Identifier) from search results
+
+### Jira
+
+- `getJiraIssue` - Get issue details by key or ID
+- `createJiraIssue` - Create new issues
+- `editJiraIssue` - Update existing issues
+- `transitionJiraIssue` - Change issue status
+- `addCommentToJiraIssue` - Add comments to issues
+- `addWorklogToJiraIssue` - Log work time
+- `searchJiraIssuesUsingJql` - Search with JQL queries
+- `getTransitionsForJiraIssue` - Get available status transitions
+- `getVisibleJiraProjects` - List accessible projects
+- `getJiraProjectIssueTypesMetadata` - Get issue types for a project
+- `getJiraIssueTypeMetaWithFields` - Get field metadata for issue type
+- `getJiraIssueRemoteIssueLinks` - Get remote links
+- `lookupJiraAccountId` - Find user account IDs
+
+### Confluence
+
+- `getConfluencePage` - Get page content by ID
+- `createConfluencePage` - Create new pages
+- `updateConfluencePage` - Update existing pages
+- `searchConfluenceUsingCql` - Search with CQL queries
+- `getConfluenceSpaces` - List spaces
+- `getPagesInConfluenceSpace` - List pages in a space
+- `getConfluencePageDescendants` - Get child pages
+- `getConfluencePageFooterComments` - Get footer comments
+- `getConfluencePageInlineComments` - Get inline comments
+- `createConfluenceFooterComment` - Add footer comment
+- `createConfluenceInlineComment` - Add inline comment on specific text
+
+### Utility
+
+- `atlassianUserInfo` - Get current user info
+- `getAccessibleAtlassianResources` - Get cloudId for API calls
+
+## Quick Start
+
+### 1. Configuration
+
+The MCP server uses OAuth 2.1 - no API tokens needed. Configuration in `mcp.json`:
+
+```json
+{
+  "jira": {
+    "command": "npx",
+    "args": ["-y", "mcp-remote", "https://mcp.atlassian.com/v1/sse"]
+  }
+}
+```
+
+### 2. Get Cloud ID
+
+Most tools require a `cloudId`. Get it from your site URL or use the utility:
+
+```typescript
+// Get accessible resources and cloudId
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "getAccessibleAtlassianResources"),
+  (arguments = "{}"),
+);
+```
+
+Or use your site URL directly as cloudId (e.g., `"ibet.atlassian.net"`).
+
+### 3. Use MCP Tools
+
+```typescript
+// Universal search (recommended for discovery)
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "search"),
+  (arguments = '{"query": "authentication bug"}'),
+);
+
+// Get issue details
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "getJiraIssue"),
+  (arguments = '{"cloudId": "your-site.atlassian.net", "issueIdOrKey": "PROJ-123"}'),
+);
+
+// Search with JQL
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "searchJiraIssuesUsingJql"),
+  (arguments = '{"cloudId": "your-site.atlassian.net", "jql": "project = PROJ AND status = Open"}'),
+);
+
+// Create issue
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "createJiraIssue"),
+  (arguments =
+    '{"cloudId": "your-site.atlassian.net", "projectKey": "PROJ", "issueTypeName": "Bug", "summary": "Login fails on mobile"}'),
+);
+
+// Transition issue status
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "transitionJiraIssue"),
+  (arguments =
+    '{"cloudId": "your-site.atlassian.net", "issueIdOrKey": "PROJ-123", "transition": {"id": "21"}}'),
+);
+
+// Get Confluence page
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "getConfluencePage"),
+  (arguments = '{"cloudId": "your-site.atlassian.net", "pageId": "123456789"}'),
+);
+
+// Search Confluence with CQL
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "searchConfluenceUsingCql"),
+  (arguments = '{"cloudId": "your-site.atlassian.net", "cql": "title ~ \"Onboarding\""}'),
+);
+```
+
+## Common Workflows
+
+### Daily Standup
+
+```typescript
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "searchJiraIssuesUsingJql"),
+  (arguments =
+    '{"cloudId": "your-site.atlassian.net", "jql": "assignee = currentUser() AND updated >= -1d"}'),
+);
+```
+
+### Bug Triage
+
+```typescript
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "searchJiraIssuesUsingJql"),
+  (arguments =
+    '{"cloudId": "your-site.atlassian.net", "jql": "type = Bug AND priority in (High, Critical) AND status != Done"}'),
+);
+```
+
+### Sprint Planning
+
+```typescript
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "searchJiraIssuesUsingJql"),
+  (arguments =
+    '{"cloudId": "your-site.atlassian.net", "jql": "project = PROJ AND sprint in openSprints()"}'),
+);
+```
+
+### Quick Discovery with Rovo Search
+
+```typescript
+// Best for finding content when you don't know exact location
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "search"),
+  (arguments = '{"query": "authentication implementation"}'),
+);
+
+// Then fetch details using ARI from results
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "fetch"),
+  (arguments = '{"id": "ari:cloud:jira:cloudId:issue/10107"}'),
+);
+```
+
+## JQL Examples
+
+```sql
+-- My open issues
+assignee = currentUser() AND status != Done
+
+-- High priority bugs
+project = PROJ AND type = Bug AND priority in (High, Critical)
+
+-- Recently updated
+project = PROJ AND updated >= -7d
+
+-- Current sprint
+project = PROJ AND sprint in openSprints()
+
+-- Unassigned in backlog
+project = PROJ AND assignee is EMPTY AND status = "To Do"
+```
+
+## CQL Examples (Confluence)
+
+```sql
+-- Pages with title containing "guide"
+title ~ "guide"
+
+-- Pages in specific space
+space = "TEAM" AND type = page
+
+-- Recently modified
+lastModified >= now("-7d")
+
+-- Pages by creator
+creator = currentUser()
+```
+
+## Content Format Options
+
+For Confluence pages, you can specify content format:
+
+- `"markdown"` - Markdown format (easier to read/write)
+- `"adf"` - Atlassian Document Format (native format)
+
+```typescript
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "getConfluencePage"),
+  (arguments =
+    '{"cloudId": "your-site.atlassian.net", "pageId": "123456", "contentFormat": "markdown"}'),
+);
+```
+
+## Transition Workflow
+
+To change issue status, first get available transitions:
+
+```typescript
+// 1. Get available transitions
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "getTransitionsForJiraIssue"),
+  (arguments = '{"cloudId": "your-site.atlassian.net", "issueIdOrKey": "PROJ-123"}'),
+);
+
+// 2. Use transition ID to change status
+skill_mcp(
+  (skill_name = "jira"),
+  (tool_name = "transitionJiraIssue"),
+  (arguments =
+    '{"cloudId": "your-site.atlassian.net", "issueIdOrKey": "PROJ-123", "transition": {"id": "31"}}'),
+);
+```
+
+## Resources
+
+- GitHub: https://github.com/atlassian/atlassian-mcp-server
+- Docs: https://www.atlassian.com/platform/remote-mcp-server
+- Admin Guide: https://support.atlassian.com/security-and-access-policies/docs/understand-atlassian-rovo-mcp-server/

package/.codex/skills/jira/mcp.json

@@ -0,0 +1,6 @@
+{
+	"jira": {
+		"command": "npx",
+		"args": ["-y", "mcp-remote", "https://mcp.atlassian.com/v1/sse"]
+	}
+}