chore: regenerate .codecortex/ knowledge and inject CLAUDE.md

Dogfoods the v0.6.0 release + the Apr 19 manifest fix. Refreshed
cortex.yaml is clean (no absolute root path). Adds missing
AGENT.md and hotspots.md that were not committed with v0.6.0.

Knowledge stats: 70 files, 1549 symbols, 7 modules, 52 commits,
21 hidden deps.

Author: rushikeshmore

.codecortex/AGENT.md

@@ -0,0 +1,28 @@
+# CodeCortex — Codebase Navigation & Risk Tools
+
+This project uses CodeCortex. It gives you a pre-built map of the codebase — architecture, dependencies, risk areas, hidden coupling. Use it to navigate to the right files, then read those files with your normal tools.
+
+**CodeCortex finds WHERE to look. You still read the code.**
+
+## Navigation (start here)
+- `get_project_overview` — architecture, modules, risk map. Call this first.
+- `lookup_symbol` — precise symbol lookup with kind + file path filters. Use when you know exactly what you're looking for (e.g., "all interfaces in gateway/").
+- `get_dependency_graph` — import/export graph filtered by file or module.
+
+## When to use grep instead
+- "How does X work?" → grep (searches file contents)
+- "Find all usage of X" → grep (finds every occurrence)
+- "Where is X defined?" → `lookup_symbol` (finds definitions with filters)
+
+## Before Editing (ALWAYS call these)
+- `get_edit_briefing` — co-change risks, hidden dependencies, bug history for files you plan to edit. Prevents bugs from files that secretly change together.
+- `get_change_coupling` — files that historically change together. Missing one causes bugs.
+
+## Static Knowledge (read directly, no tool needed)
+- `.codecortex/modules/*.md` — module docs (purpose, deps, API)
+- `.codecortex/hotspots.md` — files ranked by risk (churn + coupling + bugs)
+- `.codecortex/patterns.md` — coding conventions
+- `.codecortex/decisions/*.md` — architectural decision records
+
+## Response Detail Control
+Most tools accept `detail: "brief"` (default) or `"full"`. Use brief for exploration, full only when you need exhaustive data.

.codecortex/constitution.md

@@ -5,60 +5,60 @@
 ## Project
 - **Name:** codecortex-ai
 - **Languages:** typescript
-- **Files:** 57
-- **Symbols:** 1313
+- **Files:** 70
+- **Symbols:** 1549
 - **Modules:** 7
-- **Last updated:** 2026-03-07T20:43:20.651Z
+- **Last updated:** 2026-04-21T10:10:23.420Z
 
 ## Architecture
 
 **Entry points:** `dist/cli/index.js`
 
-**Modules:**
-- **cli** (13 files, 1569 lines) — typescript
-- **core** (11 files, 974 lines) — typescript
+**Modules (7):**
+- **cli** (14 files, 1661 lines) — typescript
+- **core** (14 files, 1654 lines) — typescript
 - **extraction** (4 files, 1149 lines) — typescript
-- **git** (3 files, 359 lines) — typescript
-- **mcp** (3 files, 708 lines) — typescript
-- **types** (2 files, 226 lines) — typescript
-- **utils** (3 files, 210 lines) — typescript
+- **mcp** (4 files, 590 lines) — typescript
+- **git** (3 files, 440 lines) — typescript
+- **utils** (4 files, 283 lines) — typescript
+- **types** (2 files, 228 lines) — typescript
 
-**External dependencies:** `node:path`, `node:fs`, `simple-git`, `node:child_process`, `commander`, `node:module`, `node:os`, `tree-sitter`, `@modelcontextprotocol/sdk`, `zod`, `yaml`, `vitest`, `express`, `tsup`
+**External dependencies (14):** `node:path`, `node:fs`, `simple-git`, `node:child_process`, `commander`, `node:module`, `node:os`, `tree-sitter`, `@modelcontextprotocol/sdk`, `zod`, `yaml`, `vitest`, `express`, `tsup`
 
 ## Risk Map
 
 **Hottest files (most changes):**
-- `README.md` — 12 changes, VOLATILE
-- `src/mcp/server.ts` — 10 changes, VOLATILE
-- `CLAUDE.md` — 7 changes, STABILIZING
-- `tests/extraction/parser.test.ts` — 6 changes, STABILIZING
-- `src/extraction/parser.ts` — 5 changes, STABILIZING
+- `README.md` — 17 changes, MODERATE
+- `src/mcp/server.ts` — 14 changes, MODERATE
+- `CLAUDE.md` — 12 changes, MODERATE
+- `src/cli/commands/init.ts` — 9 changes, VOLATILE
+- `src/cli/commands/update.ts` — 7 changes, MODERATE
 
 **Hidden dependencies (co-change but no import):**
-- `src/cli/commands/init.ts` ↔ `src/cli/commands/update.ts` — 5 co-changes (100%)
-- `.gitignore` ↔ `src/cli/commands/init.ts` — 3 co-changes (60%)
-- `.gitignore` ↔ `src/cli/commands/update.ts` — 3 co-changes (60%)
-- `src/cli/commands/init.ts` ↔ `tsup.config.ts` — 3 co-changes (60%)
-- `src/cli/commands/update.ts` ↔ `tsup.config.ts` — 3 co-changes (60%)
+- `src/cli/commands/init.ts` ↔ `src/cli/commands/update.ts` — 7 co-changes (78%)
+- `src/mcp/tools/read.ts` ↔ `src/mcp/tools/write.ts` — 4 co-changes (67%)
+- `src/core/agent-instructions.ts` ↔ `src/mcp/tools/read.ts` — 3 co-changes (50%)
+- `src/core/constitution.ts` ↔ `src/mcp/tools/read.ts` — 3 co-changes (50%)
+- `src/git/temporal.ts` ↔ `src/mcp/tools/read.ts` — 3 co-changes (50%)
 
 **Bug-prone files:**
-- `README.md` — 3 fix commits
-  - v0.4.3 — Node 20-22 engine restriction, fix broken README link
+- `CLAUDE.md` — 4 fix commits
+  - revert to "knowledge layer" positioning, add cold-start framing
   - remove tree-sitter-liquid git dep that broke npm installs (v0.4.2)
-  - Go type extraction, docs cleanup, npm publish as codecortex-ai
-- `src/mcp/server.ts` — 3 fix commits
+  - align version and language count across all surfaces
+- `README.md` — 4 fix commits
+  - revert to "knowledge layer" positioning, add cold-start framing
   - v0.4.3 — Node 20-22 engine restriction, fix broken README link
   - remove tree-sitter-liquid git dep that broke npm installs (v0.4.2)
-  - align version and language count across all surfaces
-- `CLAUDE.md` — 3 fix commits
+- `src/mcp/server.ts` — 4 fix commits
+  - revert to "knowledge layer" positioning, add cold-start framing
+  - v0.4.3 — Node 20-22 engine restriction, fix broken README link
   - remove tree-sitter-liquid git dep that broke npm installs (v0.4.2)
-  - align version and language count across all surfaces
-  - Go type extraction, docs cleanup, npm publish as codecortex-ai
 
 ## Available Knowledge
 
 **Module docs:** `cli`, `core`, `extraction`, `git`, `mcp`, `types`, `utils`
 
-Use `get_module_context` to deep-dive into any module.
+Read `.codecortex/modules/*.md` directly for module deep-dives.
 Use `get_change_coupling` before editing a file to check what else must change.
 Use `lookup_symbol` to find any function, type, or class.

.codecortex/cortex.yaml

@@ -1,12 +1,13 @@
 version: 1.0.0
 project: codecortex-ai
-generated: 2026-03-07T12:52:20.783Z
-lastUpdated: 2026-03-07T20:43:20.651Z
+generated: 2026-04-21T10:10:23.420Z
+lastUpdated: 2026-04-21T10:10:23.420Z
 languages:
   - typescript
-totalFiles: 57
-totalSymbols: 1313
+totalFiles: 70
+totalSymbols: 1549
 totalModules: 7
+projectSize: small
 tiers:
   hot:
     - cortex.yaml

.codecortex/decisions/initialized-codecortex-for-codebase-knowledge.md

@@ -0,0 +1,19 @@
+# Decision: Initialized CodeCortex for codebase knowledge
+
+**Date:** 2026-04-21
+**Status:** accepted
+
+## Context
+AI agents need persistent knowledge to avoid re-learning the codebase each session.
+
+## Decision
+Using CodeCortex to pre-analyze symbols, dependencies, coupling, and patterns.
+
+## Alternatives Considered
+- Manual CLAUDE.md only
+- No codebase context for agents
+
+## Consequences
+- AI agents start with knowledge
+- .codecortex/ added to repo
+- Knowledge needs periodic update via codecortex update

.codecortex/graph.json

@@ -0,0 +1,38 @@
+# Risk-Ranked Files
+
+> Auto-generated by CodeCortex. 52 commits analyzed over 90 days.
+
+| File | Changes | Couplings | Bugs | Risk | Stability |
+|------|---------|-----------|------|------|-----------|
+| `src/mcp/server.ts` | 14 | 9 | 4 | 30.08 | moderate |
+| `README.md` | 17 | 0 | 4 | 29 | moderate |
+| `src/cli/commands/init.ts` | 9 | 17 | 1 | 24.54 | volatile |
+| `CLAUDE.md` | 12 | 0 | 4 | 24 | moderate |
+| `src/cli/commands/update.ts` | 7 | 13 | 0 | 19.16 | moderate |
+| `src/mcp/tools/read.ts` | 6 | 11 | 0 | 16.8 | moderate |
+| `src/extraction/parser.ts` | 5 | 6 | 1 | 14.32 | moderate |
+| `src/extraction/symbols.ts` | 4 | 6 | 1 | 14.22 | moderate |
+| `src/git/temporal.ts` | 5 | 5 | 1 | 13.42 | moderate |
+| `src/extraction/calls.ts` | 3 | 6 | 0 | 11.22 | moderate |
+| `src/extraction/imports.ts` | 3 | 6 | 0 | 11.22 | moderate |
+| `tsup.config.ts` | 3 | 6 | 0 | 11.22 | moderate |
+| `src/types/index.ts` | 4 | 4 | 1 | 10.58 | moderate |
+| `src/core/discovery.ts` | 4 | 3 | 1 | 9.72 | moderate |
+| `tests/extraction/parser.test.ts` | 6 | 0 | 1 | 9 | moderate |
+| `src/mcp/tools/write.ts` | 4 | 5 | 0 | 8.48 | moderate |
+| `src/core/manifest.ts` | 3 | 2 | 1 | 8.16 | moderate |
+| `src/cli/index.ts` | 6 | 3 | 0 | 7.94 | moderate |
+| `src/core/constitution.ts` | 4 | 4 | 0 | 7.16 | moderate |
+| `src/core/agent-instructions.ts` | 3 | 3 | 0 | 6.42 | moderate |
+| `tests/core/agent-instructions.test.ts` | 3 | 3 | 0 | 6.42 | moderate |
+| `tests/fixtures/setup.ts` | 3 | 0 | 1 | 6 | moderate |
+| `src/core/graph.ts` | 3 | 0 | 1 | 6 | moderate |
+| `src/utils/files.ts` | 3 | 0 | 1 | 6 | moderate |
+| `.gitignore` | 4 | 2 | 0 | 5.52 | moderate |
+| `tests/mcp/read-tools.test.ts` | 4 | 2 | 0 | 5.42 | moderate |
+| `tests/mcp/simulation.test.ts` | 3 | 1 | 0 | 5 | moderate |
+| `tests/mcp/write-tools.test.ts` | 3 | 1 | 0 | 5 | moderate |
+| `.codecortex/cortex.yaml` | 2 | 0 | 1 | 5 | stable |
+| `tests/extraction/symbols.test.ts` | 2 | 0 | 1 | 5 | very_stable |
+
+Generated: 2026-04-21T10:10:23.419Z

.codecortex/hotspots.md

@@ -2,7 +2,7 @@
 
 **Type:** node
 **Languages:** typescript
-**Files:** 55
+**Files:** 70
 
 ## Entry Points
 - `dist/cli/index.js`
@@ -16,91 +16,9 @@
 - **types**
 - **utils**
 
-## File Map
+## Directory Summary
+- **src/** — 45 files
+- **tests/** — 23 files
+- **./** — 2 files
 
-### ./
-- tsup.config.ts
-- vitest.config.ts
-
-### src/cli/
-- grouped-help.ts
-- index.ts
-
-### src/cli/commands/
-- hook.ts
-- hotspots.ts
-- init.ts
-- modules.ts
-- search.ts
-- serve.ts
-- status.ts
-- symbols.ts
-- update.ts
-- upgrade.ts
-
-### src/cli/utils/
-- version-check.ts
-
-### src/core/
-- constitution.ts
-- decisions.ts
-- discovery.ts
-- graph.ts
-- manifest.ts
-- module-gen.ts
-- modules.ts
-- patterns.ts
-- search.ts
-- sessions.ts
-
-### src/extraction/
-- calls.ts
-- imports.ts
-- parser.ts
-- symbols.ts
-
-### src/git/
-- diff.ts
-- history.ts
-- temporal.ts
-
-### src/mcp/
-- server.ts
-
-### src/mcp/tools/
-- read.ts
-- write.ts
-
-### src/types/
-- index.ts
-- schema.ts
-
-### src/utils/
-- files.ts
-- markdown.ts
-- yaml.ts
-
-### tests/cli/
-- hook.test.ts
-- version-check.test.ts
-
-### tests/core/
-- decisions.test.ts
-- graph.test.ts
-- search.test.ts
-- sessions.test.ts
-
-### tests/extraction/
-- calls.test.ts
-- imports.test.ts
-- parser.test.ts
-- symbols.test.ts
-
-### tests/fixtures/
-- setup.ts
-
-### tests/mcp/
-- read-tools.test.ts
-- server.test.ts
-- simulation.test.ts
-- write-tools.test.ts
+> For detailed file lists, use `search_knowledge` or `get_dependency_graph` MCP tools.

.codecortex/overview.md

@@ -1,3 +1,3 @@
 # Coding Patterns
 
-No patterns recorded yet. Use `update_patterns` to add patterns.
+No patterns recorded yet. Edit this file directly to add patterns.