project-graph-mcp 2.0.0 → 2.1.0

package/README.md

@@ -4,10 +4,16 @@
 
 # project-graph-mcp
 
-An MCP server that parses your source code into a **10-50x compressed skeleton** — classes, functions, imports, and dependencies in a minified JSON. Agents navigate the graph using `expand`, `deps`, and `usages` without reading irrelevant files. The **AI Context Layer** compresses an entire codebase into ~1700 tokens (97% savings) with a single `get_ai_context` call. Supports **monorepo scanning** and **streaming analysis** for large codebases.
+**Maximize your AI agent's context window.** An MCP server that lets agents read and edit your codebase in **compact mode** — minified source with all variable names preserved. Code tokens drop **↓40%**, and `.ctx` documentation is injected only in the focus zone. Fewer tokens per file → more files fit in context → **deeper understanding of your codebase**.
+
+![Expanded view — formatted code with JSDoc, 28+ lines per function](docs/img/explorer-expanded.jpg)
+
+![Compact mode — same file, 14 lines total, ↓40% tokens. Agents read and edit this directly.](docs/img/explorer-compact.jpg)
+
+Includes a built-in [Web Dashboard](#web-dashboard) (`npx project-graph-mcp serve`) to visualize token metrics and compact ⇄ raw code in real-time.
 
 > [!TIP]
-> **18 MCP tools.** Add one line to your MCP config and the server downloads itself on the next IDE restart.
+> **18 MCP tools, zero config.** Add one line to your MCP config and the server downloads itself on the next IDE restart.
 
 ### Project Skeleton (10-50x compression)
 
@@ -54,7 +60,7 @@ One call loads everything an agent needs to understand a project:
 
 ```javascript
 get_ai_context({ path: "src/" })
-// → { skeleton, docs, totalTokens: 1742, savings: "97%" }
+// → { skeleton, docs, totalTokens: 3150, savings: "93%" }
 ```
 
 - **Code compression** — Terser-minified source with export legend headers (20-55% per file)
@@ -107,16 +113,13 @@ get_focus_zone({ path: ".", useGitDiff: true })
 // → Context for recently changed files only
 ```
 
-**Real-world token budget** (45-file project):
+**Real-world token budget** (this project's own benchmark, 45 files):
 
 ```
-Traditional (raw sources):     64K tok — read everything expanded
-Overview (compact, no .ctx):   47K tok — 27% savings, full project
-Focus (compact + 3 files ctx): 47.6K tok — same savings + semantic descriptions
+Skeleton + docs only:          3.2K tok — 93% savings, full project overview
+Compact source (agent reads): 46.9K tok — 20-55% savings per file
 ```
 
-Compact code saves **27% on average** (34-38% for typical files) by stripping whitespace and comments while preserving all names. The `.ctx` cost is **per-file** (~200 tok each) and only loaded for the focus area — the agent gets typed signatures and descriptions that the raw source never had.
-
 **Per-file metrics breakdown:**
 
 | Layer | What | Tokens |
@@ -124,22 +127,31 @@ Compact code saves **27% on average** (34-38% for typical files) by stripping wh
 | Code (compact .js) | Minified source, all names preserved | codeTok |
 | Context (.ctx) | AST signatures, types, descriptions | ctxTok |
 | Total (focus mode) | What agent reads when focusing | codeTok + ctxTok |
-| Expanded (beautified) | What a human would read (raw source) | expanded |
 
 ### Compact Code Architecture
 
-Three modes for AI-native codebase editing — configure per project via `.context/config.json`:
+Two modes for AI-native codebase editing — configure per project via `.context/config.json`:
+
+| Mode | Storage | Agent reads/writes | Human reviews |
+|------|---------|-------------------|---------------|
+| **1 — Compact** ⭐ | Minified JS | `src/` directly | `.expanded/` cache |
+| **2 — Full** | Formatted JS | compressed view | `src/` directly |
+
+**Mode 1 — Compact** (recommended for AI-first projects):
+
+Source of truth is compact code. Agents read and write it directly — saving tokens in **both directions** (input and output). Since output tokens cost 3-5x more than input, compact output is the biggest cost saving. Humans review via auto-generated `.expanded/` cache with restored names and injected JSDoc.
 
-| Mode | Storage | Agent reads | Agent edits |
-|------|---------|-------------|-------------|
-| **1 — Native Compact** | Minified JS | Files directly | Files directly |
-| **2 — Full Storage** (default) | Formatted JS | `get_compressed_file` | `edit_compressed` |
-| **3 — IDE Virtual** | Minified JS | IDE renders full view | IDE handles mapping |
+```javascript
+// Agent reads and edits compact source directly (20-55% fewer tokens both ways)
+// After edits, validate and generate human-readable cache:
+compact({ action: "validate_pipeline", path: ".", strict: true })
+compact({ action: "expand_project", path: "." })
+```
 
-**Mode 2 workflow** (recommended):
+**Mode 2 — Full** (for existing projects, no refactoring needed):
 
 ```javascript
-// 1. Read compressed view (saves 20-55% tokens)
+// 1. Read compressed view (saves input tokens only)
 get_compressed_file({ path: "src/parser.js" })
 
 // 2. Edit by symbol name — server finds it via AST
@@ -153,6 +165,14 @@ edit_compressed({
 validate_ctx_contracts({ path: "." })
 ```
 
+**Migrating from Full to Compact:**
+
+```bash
+# Ensure git is clean, then run automated migration
+npx project-graph-mcp compact-migrate .
+# → compacts all JS, generates @names in .ctx, sets mode 1, validates
+```
+
 **`.ctx` typed signatures** — JSDoc types extracted into compact format:
 
 ```
@@ -160,8 +180,11 @@ parseFile(code:string,filename:string)→Promise<ParseResult>→parse,walk|parse
 ```
 
 ```bash
+# Check current mode
+npx project-graph-mcp mode .
+
 # Set project mode
-npx project-graph-mcp set-mode . 2
+npx project-graph-mcp set-mode . 1
 
 # Validate .ctx documentation matches source
 npx project-graph-mcp validate-ctx . --strict
@@ -226,6 +249,8 @@ Every project-graph-mcp instance includes a built-in web UI at `http://localhost
 - **Health panel** — analysis results
 - **Live monitor** — real-time agent activity via WebSocket
 
+
+
 With the optional gateway, all projects are accessible under `http://project-graph.local/{project-name}/`.
 
 ### Compression Metrics
@@ -263,20 +288,13 @@ Every tool response includes contextual coaching — if the agent finds a massiv
 
 ## Quick Start
 
-Add to your IDE's MCP configuration:
+Generate the MCP config for your IDE (with correct paths):
 
-```json
-{
-  "mcpServers": {
-    "project-graph": {
-      "command": "npx",
-      "args": ["-y", "project-graph-mcp"]
-    }
-  }
-}
+```bash
+npx -y project-graph-mcp config
 ```
 
-Restart your IDE — project-graph-mcp will be downloaded and started automatically.
+Copy the output JSON into your IDE's MCP config file, then restart.
 
 #### Grouped Tools (v2.0)
 
@@ -333,7 +351,9 @@ npx project-graph-mcp docs src/           # Project docs (doc-dialect)
 npx project-graph-mcp generate-ctx src/   # Generate .context/ docs
 npx project-graph-mcp validate-ctx .      # Validate .ctx ↔ source
 npx project-graph-mcp mode .             # Show current editing mode
-npx project-graph-mcp set-mode . 2       # Set mode (1/2/3)
+npx project-graph-mcp compact-migrate .  # Migrate formatted -> compact (git must be clean)
+npx project-graph-mcp set-mode . 1       # Set mode (1=compact*, 2=full)
+npx project-graph-mcp serve .            # Start web dashboard
 npx project-graph-mcp help                # All commands
 ```
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "project-graph-mcp",
-  "version": "2.0.0",
+  "version": "2.1.0",
   "type": "module",
   "description": "MCP server for AI agents — project graph, code quality analysis, visual web explorer. JS, TS, Python, Go.",
   "main": "src/network/server.js",

package/src/.project-graph-cache.json

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package/src/cli/cli-handlers.js

@@ -1,4 +1,4 @@
 // @ctx .context/src/cli/cli-handlers.ctx
-import{getSkeleton as r,expand as e,deps as s,usages as t}from"../mcp/tools.js";import{getPendingTests as a,getTestSummary as n}from"../analysis/test-annotations.js";import{getFilters as o}from"../core/filters.js";import{getInstructions as c}from"../compact/instructions.js";import{getUndocumentedSummary as i}from"../analysis/undocumented.js";import{getDeadCode as d}from"../analysis/dead-code.js";import{generateJSDoc as l}from"../analysis/jsdoc-generator.js";import{getSimilarFunctions as m}from"../analysis/similar-functions.js";import{getComplexity as g}from"../analysis/complexity.js";import{getLargeFiles as u}from"../analysis/large-files.js";import{getOutdatedPatterns as p}from"../analysis/outdated-patterns.js";import{getFullAnalysis as y}from"../analysis/full-analysis.js";import{compressFile as h}from"../compact/compress.js";import{getProjectDocs as f,generateContextFiles as j}from"../compact/doc-dialect.js";import{getGraph as A}from"../mcp/tools.js";import{parseProject as P}from"../core/parser.js";import{resolvePath as q}from"../core/workspace.js";import{checkJSDocConsistency as x}from"../analysis/jsdoc-checker.js";import{checkTypes as E}from"../analysis/type-checker.js";import{compactProject as b,expandProject as w}from"../compact/compact.js";import{injectJSDoc as S,stripJSDoc as U,validateCtxContracts as k}from"../compact/ctx-to-jsdoc.js";import{getConfig as C,setConfig as v,getModeDescription as D,getModeWorkflow as I}from"../compact/mode-config.js";function getArg(r,e){const s=r.find(r=>r.startsWith(`--${e}=`));return s?s.split("=")[1]:void 0}
+import{getSkeleton as r,expand as e,deps as s,usages as t}from"../mcp/tools.js";import{getPendingTests as a,getTestSummary as n}from"../analysis/test-annotations.js";import{getFilters as o}from"../core/filters.js";import{getInstructions as c}from"../compact/instructions.js";import{getUndocumentedSummary as i}from"../analysis/undocumented.js";import{getDeadCode as d}from"../analysis/dead-code.js";import{generateJSDoc as l}from"../analysis/jsdoc-generator.js";import{getSimilarFunctions as m}from"../analysis/similar-functions.js";import{getComplexity as g}from"../analysis/complexity.js";import{getLargeFiles as u}from"../analysis/large-files.js";import{getOutdatedPatterns as p}from"../analysis/outdated-patterns.js";import{getFullAnalysis as y}from"../analysis/full-analysis.js";import{compressFile as h}from"../compact/compress.js";import{getProjectDocs as f,generateContextFiles as j}from"../compact/doc-dialect.js";import{getGraph as A}from"../mcp/tools.js";import{parseProject as P}from"../core/parser.js";import{resolvePath as q}from"../core/workspace.js";import{checkJSDocConsistency as x}from"../analysis/jsdoc-checker.js";import{checkTypes as E}from"../analysis/type-checker.js";import{compactProject as b,expandProject as w}from"../compact/compact.js";import{injectJSDoc as S,stripJSDoc as U,validateCtxContracts as k}from"../compact/ctx-to-jsdoc.js";import{getConfig as C,setConfig as v,getModeDescription as D,getModeWorkflow as I}from"../compact/mode-config.js";import{compactMigrate as M}from"../compact/compact-migrate.js";function getArg(r,e){const s=r.find(r=>r.startsWith(`--${e}=`));return s?s.split("=")[1]:void 0}
 function getPath(r){const e=r.find(r=>!r.startsWith("--"))||".";return q(e)}
-export const CLI_HANDLERS={skeleton:{requiresArg:!0,argError:"Path required: skeleton <path>",handler:async e=>r(q(e[0]))},expand:{requiresArg:!0,argError:"Symbol required: expand <symbol>",handler:async r=>e(r[0])},deps:{requiresArg:!0,argError:"Symbol required: deps <symbol>",handler:async r=>s(r[0])},usages:{requiresArg:!0,argError:"Symbol required: usages <symbol>",handler:async r=>t(r[0])},pending:{handler:async r=>a(getPath(r))},summary:{handler:async r=>n(getPath(r))},filters:{handler:async()=>o()},instructions:{rawOutput:!0,handler:async()=>c()},undocumented:{handler:async r=>{const e=getArg(r,"level")||"tests";return i(getPath(r),e)}},deadcode:{handler:async r=>d(getPath(r))},jsdoc:{requiresArg:!0,argError:"Usage: jsdoc <file>",handler:async r=>l(q(r[0]))},similar:{handler:async r=>{const e=parseInt(getArg(r,"threshold"))||60;return m(getPath(r),{threshold:e})}},complexity:{handler:async r=>{const e=parseInt(getArg(r,"min"))||1,s=r.includes("--problematic");return g(getPath(r),{minComplexity:e,onlyProblematic:s})}},largefiles:{handler:async r=>{const e=r.includes("--problematic");return u(getPath(r),{onlyProblematic:e})}},outdated:{handler:async r=>{const e=r.includes("--code"),s=r.includes("--deps");return p(getPath(r),{codeOnly:e,depsOnly:s})}},analyze:{handler:async r=>{const e=r.includes("--items");return y(getPath(r),{includeItems:e})}},"jsdoc-check":{handler:async r=>x(getPath(r))},types:{handler:async r=>{const e=parseInt(getArg(r,"max"))||50;return E(getPath(r),{maxDiagnostics:e})}},compress:{requiresArg:!0,argError:"Usage: compress <file> [--no-beautify] [--no-legend]",handler:async r=>{const e=!r.includes("--no-beautify"),s=!r.includes("--no-legend");return h(q(r[0]),{beautify:e,legend:s})}},docs:{requiresArg:!0,argError:"Usage: docs <path> [--file=<filename>]",handler:async r=>{const e=q(r[0]),s=await A(e),t=r.find(r=>r.startsWith("--file="))?.split("=")[1];return f(s,e,{file:t})}},"generate-ctx":{requiresArg:!0,argError:"Usage: generate-ctx <path> [--overwrite] [--scope=focus|all]",handler:async r=>{const e=q(r[0]),s=await A(e),t=await P(e),a=r.includes("--overwrite"),n=r.find(r=>r.startsWith("--scope="))?.split("=")[1]||"all";return j(s,e,t,{overwrite:a,scope:n})}},compact:{requiresArg:!0,argError:"Usage: compact <path> [--dry-run]",handler:async r=>{const e=q(r[0]),s=r.includes("--dry-run");return b(e,{dryRun:s})}},beautify:{requiresArg:!0,argError:"Usage: beautify <path> [--dry-run]",handler:async r=>{const e=q(r[0]),s=r.includes("--dry-run");return w(e,{dryRun:s})}},"inject-jsdoc":{requiresArg:!0,argError:"Usage: inject-jsdoc <path> [--dry-run]",handler:async r=>{const e=q(r[0]),s=r.includes("--dry-run");return S(e,{dryRun:s})}},"strip-jsdoc":{requiresArg:!0,argError:"Usage: strip-jsdoc <path> [--dry-run]",handler:async r=>{const e=q(r[0]),s=r.includes("--dry-run");return U(e,{dryRun:s})}},"validate-ctx":{requiresArg:!0,argError:"Usage: validate-ctx <path> [--strict]",handler:async r=>{const e=q(r[0]),s=r.includes("--strict");return k(e,{strict:s})}},mode:{requiresArg:!0,argError:"Usage: mode <path>",handler:async r=>{const e=q(r[0]),s=C(e);return{...s,description:D(s.mode),workflow:I(s.mode)}}},"set-mode":{requiresArg:!0,argError:"Usage: set-mode <path> <1|2|3>",handler:async r=>{const e=q(r[0]),s=parseInt(r[1],10);if(!s||![1,2,3].includes(s))throw new Error("Mode must be 1, 2, or 3");return v(e,{mode:s})}}};
+export const CLI_HANDLERS={config:{rawOutput:!0,handler:async()=>{const{execSync:x}=await import("child_process");let npx;try{npx=x("which npx",{encoding:"utf-8"}).trim()}catch{npx="npx"}const cfg={mcpServers:{"project-graph":{command:npx,args:["-y","project-graph-mcp"]}}};console.log("Add this to your MCP config:\n");return JSON.stringify(cfg,null,2)}},skeleton:{requiresArg:!0,argError:"Path required: skeleton <path>",handler:async e=>r(q(e[0]))},expand:{requiresArg:!0,argError:"Symbol required: expand <symbol>",handler:async r=>e(r[0])},deps:{requiresArg:!0,argError:"Symbol required: deps <symbol>",handler:async r=>s(r[0])},usages:{requiresArg:!0,argError:"Symbol required: usages <symbol>",handler:async r=>t(r[0])},pending:{handler:async r=>a(getPath(r))},summary:{handler:async r=>n(getPath(r))},filters:{handler:async()=>o()},instructions:{rawOutput:!0,handler:async()=>c()},undocumented:{handler:async r=>{const e=getArg(r,"level")||"tests";return i(getPath(r),e)}},deadcode:{handler:async r=>d(getPath(r))},jsdoc:{requiresArg:!0,argError:"Usage: jsdoc <file>",handler:async r=>l(q(r[0]))},similar:{handler:async r=>{const e=parseInt(getArg(r,"threshold"))||60;return m(getPath(r),{threshold:e})}},complexity:{handler:async r=>{const e=parseInt(getArg(r,"min"))||1,s=r.includes("--problematic");return g(getPath(r),{minComplexity:e,onlyProblematic:s})}},largefiles:{handler:async r=>{const e=r.includes("--problematic");return u(getPath(r),{onlyProblematic:e})}},outdated:{handler:async r=>{const e=r.includes("--code"),s=r.includes("--deps");return p(getPath(r),{codeOnly:e,depsOnly:s})}},analyze:{handler:async r=>{const e=r.includes("--items");return y(getPath(r),{includeItems:e})}},"jsdoc-check":{handler:async r=>x(getPath(r))},types:{handler:async r=>{const e=parseInt(getArg(r,"max"))||50;return E(getPath(r),{maxDiagnostics:e})}},compress:{requiresArg:!0,argError:"Usage: compress <file> [--no-beautify] [--no-legend]",handler:async r=>{const e=!r.includes("--no-beautify"),s=!r.includes("--no-legend");return h(q(r[0]),{beautify:e,legend:s})}},docs:{requiresArg:!0,argError:"Usage: docs <path> [--file=<filename>]",handler:async r=>{const e=q(r[0]),s=await A(e),t=r.find(r=>r.startsWith("--file="))?.split("=")[1];return f(s,e,{file:t})}},"generate-ctx":{requiresArg:!0,argError:"Usage: generate-ctx <path> [--overwrite] [--scope=focus|all]",handler:async r=>{const e=q(r[0]),s=await A(e),t=await P(e),a=r.includes("--overwrite"),n=r.find(r=>r.startsWith("--scope="))?.split("=")[1]||"all";return j(s,e,t,{overwrite:a,scope:n})}},compact:{requiresArg:!0,argError:"Usage: compact <path> [--dry-run]",handler:async r=>{const e=q(r[0]),s=r.includes("--dry-run");return b(e,{dryRun:s})}},beautify:{requiresArg:!0,argError:"Usage: beautify <path> [--dry-run]",handler:async r=>{const e=q(r[0]),s=r.includes("--dry-run");return w(e,{dryRun:s})}},"inject-jsdoc":{requiresArg:!0,argError:"Usage: inject-jsdoc <path> [--dry-run]",handler:async r=>{const e=q(r[0]),s=r.includes("--dry-run");return S(e,{dryRun:s})}},"strip-jsdoc":{requiresArg:!0,argError:"Usage: strip-jsdoc <path> [--dry-run]",handler:async r=>{const e=q(r[0]),s=r.includes("--dry-run");return U(e,{dryRun:s})}},"validate-ctx":{requiresArg:!0,argError:"Usage: validate-ctx <path> [--strict]",handler:async r=>{const e=q(r[0]),s=r.includes("--strict");return k(e,{strict:s})}},mode:{requiresArg:!0,argError:"Usage: mode <path>",handler:async r=>{const e=q(r[0]),s=C(e);return{...s,description:D(s.mode),workflow:I(s.mode)}}},"compact-migrate":{requiresArg:!0,argError:"Usage: compact-migrate <path>",handler:async r=>{const e=q(r[0]),s=r.includes("--dry-run");return M(e,{dryRun:s})}},"set-mode":{requiresArg:!0,argError:"Usage: set-mode <path> <1|2>",handler:async r=>{const e=q(r[0]),s=parseInt(r[1],10);if(!s||![1,2].includes(s))throw new Error("Mode must be 1 (compact) or 2 (full)");return v(e,{mode:s})}}};

package/src/cli/cli.js

@@ -1,5 +1,5 @@
 // @ctx .context/src/cli/cli.ctx
 import{CLI_HANDLERS as e}from"./cli-handlers.js";
-export function printHelp(){console.log("\nproject-graph-mcp - MCP server for AI agents\n\nUsage:\n  npx project-graph-mcp                  Start MCP stdio server\n  npx project-graph-mcp <command> [args] Run CLI command\n\nCommands:\n  skeleton <path>        Get compact project overview\n  expand <symbol>        Expand minified symbol (e.g., SN, SN.togglePin)\n  deps <symbol>          Get dependency tree\n  usages <symbol>        Find all usages\n  pending <path>         List pending .ctx.md test checklists\n  summary <path>         Get test progress summary\n  undocumented <path>    Find missing JSDoc (--level=tests|params|all)\n  deadcode <path>        Find unused functions/classes\n  jsdoc <file>           Generate JSDoc for file\n  similar <path>         Find similar functions (--threshold=60)\n  complexity <path>      Analyze cyclomatic complexity (--min=1)\n  largefiles <path>      Find files needing split (--problematic)\n  outdated <path>        Find legacy patterns & redundant deps\n  analyze <path>         Run ALL checks with Health Score\n  jsdoc-check <path>     Validate JSDoc ↔ function signatures\n  types <path>           Run tsc type checking (--max=50)\n  compress <file>        Compress JS file for AI (--no-beautify, --no-legend)\n  compact <path>         Compact all JS files — strips comments/whitespace (--dry-run)\n  beautify <path>        Beautify/expand all JS files — inverse of compact (--dry-run)\n  inject-jsdoc <path>    Generate JSDoc from .ctx files and inject into source\n  strip-jsdoc <path>     Strip all JSDoc blocks from source files\n  docs <path>            Get project docs in doc-dialect format (--file=<name>)\n  generate-ctx <path>    Generate .context/ docs (--overwrite --scope=focus)\n  validate-ctx <path>    Validate .ctx contracts against source AST (--strict)\n  mode <path>            Show current compact code mode and workflow\n  set-mode <path> <1|2|3> Set compact code mode (1=compact, 2=full, 3=IDE)\n  filters                Show current filter configuration\n  instructions           Show agent guidelines (JSDoc, Arch)\n  help                   Show this help\n\nExamples:\n  npx project-graph-mcp skeleton src/components\n  npx project-graph-mcp expand SN\n  npx project-graph-mcp compact src/ --dry-run\n")}
+export function printHelp(){console.log("\nproject-graph-mcp - MCP server for AI agents\n\nUsage:\n  npx project-graph-mcp                  Start MCP stdio server\n  npx project-graph-mcp <command> [args] Run CLI command\n\nCommands:\n  config                 Generate MCP config with correct paths\n  skeleton <path>        Get compact project overview\n  expand <symbol>        Expand minified symbol (e.g., SN, SN.togglePin)\n  deps <symbol>          Get dependency tree\n  usages <symbol>        Find all usages\n  pending <path>         List pending .ctx.md test checklists\n  summary <path>         Get test progress summary\n  undocumented <path>    Find missing JSDoc (--level=tests|params|all)\n  deadcode <path>        Find unused functions/classes\n  jsdoc <file>           Generate JSDoc for file\n  similar <path>         Find similar functions (--threshold=60)\n  complexity <path>      Analyze cyclomatic complexity (--min=1)\n  largefiles <path>      Find files needing split (--problematic)\n  outdated <path>        Find legacy patterns & redundant deps\n  analyze <path>         Run ALL checks with Health Score\n  jsdoc-check <path>     Validate JSDoc vs function signatures\n  types <path>           Run tsc type checking (--max=50)\n  compress <file>        Compress JS file for AI (--no-beautify, --no-legend)\n  compact <path>         Compact all JS files (--dry-run)\n  beautify <path>        Beautify/expand all JS files (--dry-run)\n  inject-jsdoc <path>    Generate JSDoc from .ctx files and inject into source\n  strip-jsdoc <path>     Strip all JSDoc blocks from source files\n  docs <path>            Get project docs in doc-dialect format (--file=<name>)\n  generate-ctx <path>    Generate .context/ docs (--overwrite --scope=focus)\n  validate-ctx <path>    Validate .ctx contracts against source AST (--strict)\n  mode <path>            Show current compact code mode and workflow\n  compact-migrate <path> Migrate formatted source to compact mode (git must be clean)\n  set-mode <path> <1|2>  Set mode (1=compact*, 2=full)\n  serve <path>           Start web dashboard (--port=N)\n  filters                Show current filter configuration\n  instructions           Show agent guidelines (JSDoc, Arch)\n  help                   Show this help\n\nQuick Start:\n  npx project-graph-mcp config            # Get MCP config for your IDE\n\nWeb Dashboard:\n  npx project-graph-mcp serve .          # Start at auto-assigned port\n  npx project-graph-mcp serve . --port 3000\n  # Then open http://localhost:{port}/ or http://project-graph.local/{name}/\n\nExamples:\n  npx project-graph-mcp skeleton src/components\n  npx project-graph-mcp expand SN\n  npx project-graph-mcp compact src/ --dry-run\n")}
 export async function runCLI(n,t){if(!n||"help"===n||"--help"===n||"-h"===n)return void printHelp();
 const o=e[n];o||(console.error(`Unknown command: ${n}`),console.error('Run with "help" for usage information'),process.exit(1)),o.requiresArg&&!t[0]&&(console.error(o.argError||`Argument required for: ${n}`),process.exit(1));try{const e=await o.handler(t);o.rawOutput?console.log(e):console.log(JSON.stringify(e,null,2))}catch(e){console.error("Error:",e.message),process.exit(1)}}

package/src/compact/.project-graph-cache.json

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package/src/compact/compact-migrate.js

@@ -0,0 +1,17 @@
+// @ctx .context/src/compact/compact-migrate.ctx
+import{readFileSync as R,writeFileSync as W,readdirSync as n,statSync as o,existsSync as s}from"fs";import{join as r,extname as c,relative as a,basename as i,dirname as l}from"path";import{execSync as u}from"child_process";import{compactProject as d}from"./compact.js";import{validatePipeline as m}from"./validate-pipeline.js";import{setConfig as f}from"./mode-config.js";
+const g=new Set([".js",".mjs"]),h=new Set(["node_modules",".git","vendor",".context","dev-docs",".agent",".agents",".expanded"]);
+function walkJS(e,t=e){const s=[];try{for(const a of n(e)){if(a.startsWith(".")&&"."!==a)continue;
+const n=r(e,a);o(n).isDirectory()?h.has(a)||s.push(...walkJS(n,t)):g.has(c(a).toLowerCase())&&s.push(n)}}catch{}return s}
+function checkGitClean(e){try{const t=u("git status --porcelain",{cwd:e,encoding:"utf-8"}).trim();if(t)throw new Error("Working directory is not clean. Commit or stash changes first.\n\nDirty files:\n"+t)}catch(e){if(e.message.includes("not clean"))throw e;throw new Error("Not a git repository or git not available: "+e.message)}}
+async function extractNames(e){const t=R(e,"utf-8"),n=new Set;try{const{parse:o}=await import("../../vendor/acorn.mjs"),{simple:s}=await import("../../vendor/walk.mjs"),r=o(t,{ecmaVersion:"latest",sourceType:"module"});s(r,{FunctionDeclaration(e){e.id?.name&&n.add(e.id.name)},ClassDeclaration(e){e.id?.name&&n.add(e.id.name)},VariableDeclarator(e){e.id?.name&&n.add(e.id.name)},ImportSpecifier(e){e.local?.name&&n.add(e.local.name)},ImportDefaultSpecifier(e){e.local?.name&&n.add(e.local.name)},AssignmentExpression(e){"Identifier"===e.left?.type&&n.add(e.left.name)}})}catch{const o=/(?:function\s+(\w+)|(\w+)\s*(?:=\s*(?:async\s+)?(?:function|\([^)]*\)\s*=>))|(?:const|let|var)\s+(\w+))/g;let s;while(s=o.exec(t)){const e=s[1]||s[2]||s[3];e&&e.length>1&&n.add(e)}}return[...n].filter(e=>e.length>1)}
+function buildNamesDirective(e,t){const n=t.split("\n"),o=new Set;const s=/(?:^|[^a-zA-Z_$])([a-z])(?:\s*[=,)}\];:]|$)/g;for(const e of n){let t;while(t=s.exec(e)){o.add(t[1])}}const r=new Map;for(const t of e){const e=t.charAt(0).toLowerCase();if(o.has(e)&&!r.has(e)){r.set(e,t)}}if(0===r.size)return null;return"@names "+[...r.entries()].map(([e,t])=>`${e}=${t}`).join(",")}
+function updateCtxNames(e,t,n){const o=a(n,e),s=i(o,c(o))+".ctx",u=l(o),d=r(n,".context",u,s);if(!S(d))return;try{let e=R(d,"utf-8");if(e.includes("@names")){e=e.replace(/@names .*/,t)}else{const n=e.indexOf("\n");e=-1===n?t+"\n"+e:e.slice(0,n+1)+t+"\n"+e.slice(n+1)}W(d,e,"utf-8")}catch{}}
+function S(e){return s(e)}
+export async function compactMigrate(e,t={}){const{dryRun:n=!1}=t;checkGitClean(e);
+const o=walkJS(e),p=[];for(const t of o){const n=a(e,t),o=await extractNames(t),s=R(t,"utf-8");p.push({file:n,namesCount:o.length,names:o,originalSize:s.length})}
+if(n)return{dryRun:!0,files:p.length,fileSummary:p.map(e=>({file:e.file,identifiers:e.namesCount,originalSize:e.originalSize}))};
+const v=await d(e,{dryRun:!1});for(const t of o){const n=R(t,"utf-8"),o=p.find(e=>t.endsWith(e.file));if(o&&o.names.length>0){const s=buildNamesDirective(o.names,n);s&&updateCtxNames(t,s,e)}}
+let b;try{b=await m(e,{strict:!1})}catch(e){b={status:"SKIP",reason:e.message}}
+f(e,{mode:1});
+return{migrated:!0,files:v.files,savings:v.savings,originalBytes:v.originalBytes,compactedBytes:v.compactedBytes,validation:b?.status||"SKIP",mode:"compact (1)",hint:"Run 'expand_project' to generate .expanded/ cache for human review"}}

package/src/compact/compress.js

@@ -6,7 +6,8 @@ let s="";if(t.start>0){const n=Math.max(0,t.start-500),a=e.slice(n,t.start).trim
 export async function compressFile(t,s={}){const{beautify:r=!0,legend:i=!0}=s,c=n(t).toLowerCase();if(!o.has(c))throw new Error(`Unsupported file type: ${c}. Supported: ${[...o].join(", ")}`);
 const l=e(t,"utf-8"),m=estimateTokens(l);if(!l.trim())return{code:"",legend:"",original:0,compressed:0,savings:"0%"};
 const d={compress:{dead_code:!0,drop_console:!1,passes:2},mangle:!1,module:!0,output:{beautify:r,comments:!1,semicolons:!r}};
-let p;try{const e=await a(l,d);if(e.error)throw e.error;p=e.code}catch(e){p=l.replace(/\/\*[\s\S]*?\*\//g,"").replace(/\/\/.*/g,"").replace(/\n{3,}/g,"\n\n").trim()}const f=i?extractLegend(l,t):"",u=f?`/*\n${f}\n*/\n${p}`:p,y=estimateTokens(u);return{code:u,legend:f,original:m,compressed:y,savings:`${m>0?Math.round(100*(1-y/m)):0}%`}}
+let p;try{const e=await a(l,d);if(e.error)throw e.error;p=e.code}catch(e){p=l.replace(/\/\*[\s\S]*?\*\//g,"").replace(/\/\/.*/g,"").replace(/\n{3,}/g,"\n\n").trim()}// Join consecutive import lines into single line
+p=p.replace(/(import\s.+?;)\n+(?=import\s)/g,"$1");const f=i?extractLegend(l,t):"",u=f?`/*\n${f}\n*/\n${p}`:p,y=estimateTokens(u);return{code:u,legend:f,original:m,compressed:y,savings:`${m>0?Math.round(100*(1-y/m)):0}%`}}
 export async function editCompressed(t,n,r,o={}){const{beautify:i=!0,dryRun:c=!1}=o,l=e(t,"utf-8");
 let m;try{m=s(l,{ecmaVersion:"latest",sourceType:"module",locations:!0})}catch(e){throw new Error(`Failed to parse ${t}: ${e.message}`)}const d=findSymbolRange(m,l,n);if(!d)throw new Error(`Symbol "${n}" not found in ${t}`);
 let p=l.slice(0,d.start)+r+l.slice(d.end);if(i)try{const e=await a(p,{compress:!1,mangle:!1,module:!0,output:{beautify:!0,comments:!0,semicolons:!1}});e.code&&(p=e.code)}catch{}try{s(p,{ecmaVersion:"latest",sourceType:"module"})}catch(e){throw new Error(`Edit would create invalid syntax: ${e.message}`)}if(!c){const{writeFileSync:e}=await import("fs");e(t,p,"utf-8")}return{success:!0,file:t,symbol:n,oldRange:{start:d.start,end:d.end},newLength:r.length,...c?{dryRun:!0}:{}}}

package/src/compact/mode-config.js

@@ -1,8 +1,8 @@
 // @ctx .context/src/compact/mode-config.ctx
 import{readFileSync as e,writeFileSync as t,existsSync as d,mkdirSync as o}from"fs";import{join as a,dirname as n}from"path";
 const r=".context/config.json",c={mode:2,beautify:!0,autoValidate:!1,stripJSDoc:!1};
-export function getConfig(t){const o=a(t,r);if(!d(o))return{...c};try{const t=e(o,"utf-8"),d=JSON.parse(t);return{...c,...d}}catch{return{...c}}}
+export function getConfig(t){const o=a(t,r);if(!d(o))return{...c};try{const t=e(o,"utf-8"),d=JSON.parse(t),s={...c,...d};if(![1,2].includes(s.mode)){s.mode=2}return s}catch{return{...c}}}
 export function setConfig(e,c){const i=a(e,r),s=n(i);d(s)||o(s,{recursive:!0});
-const f={...getConfig(e),...c};if(![1,2,3].includes(f.mode))throw new Error(`Invalid mode: ${f.mode}. Valid: 1 (compact), 2 (standard), 3 (hybrid)`);return t(i,JSON.stringify(f,null,2)+"\n","utf-8"),{saved:!0,path:i,config:f}}
-export function getModeDescription(e){switch(e){case 1:return"Compact — code stored minified, agent edits directly";case 2:return"Standard — code stored formatted, agent uses get_compressed_file + edit_compressed";case 3:return"Hybrid — compact source + .expanded/ cache for tooling and human review";default:return`Unknown mode: ${e}`}}
-export function getModeWorkflow(e){switch(e){case 1:return{read:"Read .js files directly (already compact)",edit:"Edit .js files directly",docs:"Read .ctx files for types and descriptions",validate:"Run validate-ctx to check .ctx ↔ AST consistency"};case 2:return{read:"Use get_compressed_file for token-efficient reading",edit:"Use edit_compressed(path, symbol, code) for AST-safe editing",docs:"Read .ctx files for types and descriptions",validate:"Run validate-ctx to check .ctx ↔ AST consistency"};case 3:return{read:"Read .js files directly (compact) for token efficiency",edit:"Use edit_compressed(path, symbol, code) → auto-regenerate .expanded/",docs:"Read .ctx files; JSDoc auto-injected into .expanded/ via expand",validate:"Run validate_pipeline → contracts + expand + AST verify",expand:"Run expand_project to regenerate .expanded/ from compact + .ctx"};default:return{read:"N/A",edit:"N/A",docs:"N/A",validate:"N/A"}}}
+const f={...getConfig(e),...c};if(![1,2].includes(f.mode))throw new Error(`Invalid mode: ${f.mode}. Valid: 1 (compact), 2 (full)`);return t(i,JSON.stringify(f,null,2)+"\n","utf-8"),{saved:!0,path:i,config:f}}
+export function getModeDescription(e){switch(e){case 1:return"Compact — minified source + .expanded/ cache for human review (recommended)";case 2:return"Full — formatted source, agents use compressed view for reading";default:return`Unknown mode: ${e}`}}
+export function getModeWorkflow(e){switch(e){case 1:return{read:"Read .js files directly (compact source = fewer tokens)",write:"Write .js files directly (compact output = cheaper output tokens)",review:".expanded/ cache with restored names + JSDoc for human review",validate:"Run validate_pipeline → contracts + expand + AST verify",expand:"Run expand_project to regenerate .expanded/ from compact + .ctx",migrate:"Run compact-migrate to convert formatted source → compact"};case 2:return{read:"Use get_compressed_file for token-efficient reading",write:"Use edit_compressed(path, symbol, code) for AST-safe editing",review:"Read source files directly (already formatted)",validate:"Run validate-ctx to check .ctx ↔ AST consistency"};default:return{read:"N/A",write:"N/A",review:"N/A",validate:"N/A"}}}

package/src/mcp/mcp-server.js

@@ -6,10 +6,10 @@ const r=new RegExp(`## ${s.topic}`,"i"),n=a.match(r);if(!n)return`Topic '${s.top
 const i=n.index;
 let c=a.indexOf("\n## ",i+1);return-1===c&&(c=a.length),a.substring(i,c).trim()}catch(e){return`Failed to read usage guide: ${e.message}`}},get_agent_instructions:()=>b(),get_undocumented:e=>k(A(e.path),e.level||"tests"),get_dead_code:e=>S(A(e.path)),generate_jsdoc:e=>e.name?R(A(e.path),e.name):$(A(e.path)),get_similar_functions:e=>F(A(e.path),{threshold:e.threshold}),get_complexity:e=>E(A(e.path),{minComplexity:e.minComplexity,onlyProblematic:e.onlyProblematic}),get_large_files:e=>C(A(e.path),{onlyProblematic:e.onlyProblematic}),get_outdated_patterns:e=>T(A(e.path),{codeOnly:e.codeOnly,depsOnly:e.depsOnly}),get_full_analysis:e=>U(A(e.path),{includeItems:e.includeItems}),get_custom_rules:()=>P(),set_custom_rule:e=>O(e.ruleSet,e.rule),check_custom_rules:e=>I(A(e.path),{ruleSet:e.ruleSet,severity:e.severity}),get_framework_reference:e=>J({framework:e.framework,path:e.path?A(e.path):void 0}),get_db_schema:e=>N(A(e.path)),get_table_usage:e=>L(A(e.path),e.table),get_db_dead_tables:e=>M(A(e.path)),get_compressed_file:e=>B(A(e.path),{beautify:e.beautify,legend:e.legend}),get_project_docs:async e=>{const t=A(e.path),s=await Q(t),o=G(s,t,{file:e.file});try{const e=await Y(t),s=W(t,e);return{docs:o,staleFiles:s.stale,freshCount:s.fresh}}catch{return{docs:o}}},generate_context_docs:async e=>{const t=A(e.path),s=await Q(t),o=await Y(t);return V(s,t,o,{overwrite:e.overwrite,scope:e.scope})},check_stale_docs:async e=>{const t=A(e.path),s=await Y(t);return W(t,s)},get_ai_context:async e=>{const t=A(e.path),s=await Z(t,{includeFiles:e.includeFiles,includeDocs:e.includeDocs,includeSkeleton:e.includeSkeleton});try{const e=await Y(t),o=W(t,e);s.staleFiles=o.stale}catch{}return s},check_jsdoc_consistency:e=>K(A(e.path)),check_types:async e=>X(A(e.path),{files:e.files,maxDiagnostics:e.maxDiagnostics}),discover_sub_projects:e=>H(A(e.path)),get_analysis_summary:e=>D(A(e.path)),compact_project:e=>ee(A(e.path),{dryRun:e.dryRun||!1}),beautify_project:e=>te(A(e.path),{dryRun:e.dryRun||!1}),validate_ctx_contracts:e=>re(A(e.path),{strict:e.strict||!1}),edit_compressed:e=>z(A(e.path),e.symbol,e.code,{beautify:!1!==e.beautify,dryRun:e.dryRun||!1}),get_mode:e=>{const t=A(e.path),s=ne(t);return{...s,description:ce(s.mode),workflow:de(s.mode)}},set_mode:e=>{const t=A(e.path),s={mode:e.mode};return void 0!==e.beautify&&(s.beautify=e.beautify),void 0!==e.autoValidate&&(s.autoValidate=e.autoValidate),void 0!==e.stripJSDoc&&(s.stripJSDoc=e.stripJSDoc),ie(t,s)},expand_file:async e=>{const s=A(e.path),o=t.dirname(t.dirname(s)),a=t.relative(o,s),r=t.basename(a,t.extname(a))+".ctx",n=t.dirname(a);
 let i=null;
-const c=t.join(o,n,r),d=t.join(o,".context",n,r);return pe(c)?i=le(c,"utf-8"):pe(d)&&(i=le(d,"utf-8")),se(s,i)},expand_project:e=>oe(A(e.path),{dryRun:e.dryRun||!1}),validate_pipeline:e=>ae(A(e.path),{strict:e.strict||!1})},_e={get_skeleton:()=>['💡 Use expand("SYMBOL") to see code for a specific class.','💡 Use deps("SYMBOL") to see architecture dependencies.',"💡 After code changes, run invalidate_cache() to refresh the graph."],expand:e=>{const t=[];return e.methods?.length>10&&t.push("💡 Large class detected. Run get_complexity() to find refactoring targets."),t.push("💡 Use deps() to see what depends on this symbol."),e.file&&t.push(`📝 No .ctx for ${e.file}? Run generate_context_docs({ scope: ["${e.file}"] }) to create documentation.`),t},deps:()=>["💡 Use usages() for cross-project reference search."],get_call_chain:e=>e.error?[]:["💡 Use expand() on intermediate steps to understand how data is passed along the chain."],invalidate_cache:()=>["✅ Cache cleared. Run get_skeleton() to rebuild the project graph."],get_dead_code:e=>{const t=["💡 Review each item before removing — some may be used dynamically."];return e.unusedExports?.length>20&&t.push('💡 Consider delegating cleanup to agent-pool: delegate_task({ prompt: "Remove dead code..." })'),t},get_full_analysis:()=>['💡 Focus on items with "critical" severity first.',"💡 Run individual tools (get_complexity, get_dead_code) for detailed breakdowns."],get_complexity:()=>["💡 Functions with complexity >10 are candidates for refactoring.","💡 Use expand() to read the function code before refactoring."],get_undocumented:()=>["💡 Use generate_jsdoc() to auto-generate documentation templates."],get_similar_functions:()=>["💡 Consider extracting duplicated logic into a shared utility."],get_pending_tests:()=>["💡 Use mark_test_passed(testId) or mark_test_failed(testId, reason) to track progress."],get_db_schema:e=>{const t=[];return e.totalTables>0?t.push(`💡 Found ${e.totalTables} tables. Use get_table_usage() to see which code reads/writes them.`):t.push("💡 No .sql schema files found. Add schema.sql or migrations/*.sql to your project."),t},get_table_usage:e=>{const t=["💡 Use get_db_dead_tables() to find tables defined in schema but never queried."];return 0===e.totalTables&&t.push("💡 No SQL queries detected. This tool finds SQL in .query(), .execute(), sql`...` patterns."),t},get_db_dead_tables:()=>["💡 Dead columns detection is best-effort — verify before removing."],get_compressed_file:e=>{const t=[`💡 Saved ${e.savings} tokens (${e.original} → ${e.compressed}).`];return t.push("💡 Use get_ai_context() for full project boot: skeleton + docs + compressed files."),e.file&&t.push(`📝 Working on ${e.file}? Run generate_context_docs({ scope: ["${e.file}"] }) to document it.`),t},get_project_docs:e=>{const t=["💡 Enrich docs by editing .context/*.ctx files — they are git-tracked.","💡 Use generate_context_docs() to create initial .ctx stubs."];return e.staleFiles?.length>0&&t.push(`⚠️ ${e.staleFiles.length} .ctx files are STALE: ${e.staleFiles.slice(0,5).join(", ")}. Run generate_context_docs({ scope: ${JSON.stringify(e.staleFiles)}, overwrite: true }) to update (descriptions will be preserved).`),t},check_stale_docs:e=>{const t=[];return e.stale?.length>0?(t.push(`⚠️ ${e.stale.length} stale: ${e.stale.join(", ")}`),t.push(`💡 Run generate_context_docs({ scope: ${JSON.stringify(e.stale)}, overwrite: true }) — existing descriptions will be preserved.`)):t.push("✅ All .ctx docs are up to date."),e.unknown>0&&t.push(`ℹ️ ${e.unknown} .ctx files without @sig header (pre-staleness format).`),t},generate_context_docs:e=>{const t=[];return e.created?.length>0&&t.push(`✅ Created ${e.created.length} .ctx files with @sig hashes.`),e.skipped?.length>0&&t.push(`ℹ️ Skipped ${e.skipped.length} existing files. Use overwrite=true to regenerate (descriptions are preserved via merge).`),e.templates&&Object.keys(e.templates).length>0&&(t.push("📝 .ctx files have {DESCRIBE} markers. To enrich automatically:"),t.push('   delegate_task({ prompt: "Enrich .context/*.ctx files — replace {DESCRIBE} with compact descriptions", skill: "doc-enricher" })'),t.push("   Or enrich manually: read source files and replace {DESCRIBE} markers with pipe-separated descriptions (max 80 chars).")),t},get_ai_context:e=>{const t=[`💡 Context loaded: ${e.totalTokens} tokens (${e.savings} savings vs ${e.vsOriginal} original).`];return t.push("💡 Use expand() to drill into specific symbols. Use get_compressed_file() for additional files."),t.push("📋 Read .context/*.ctx files for typed signatures and documentation. Check .gemini/AGENTS.md for project-specific rules."),e.staleFiles?.length>0&&t.push(`⚠️ ${e.staleFiles.length} .ctx docs are stale. Run generate_context_docs({ scope: ${JSON.stringify(e.staleFiles)}, overwrite: true }) then delegate_task({ skill: "doc-enricher" }) to update.`),t},validate_ctx_contracts:e=>{const t=[];return e.summary?.errors>0?t.push(`⚠️ ${e.summary.errors} contract violations found. Run generate_context_docs({ overwrite: true }) to regenerate .ctx files.`):t.push("✅ All .ctx contracts valid — documentation matches source."),t},edit_compressed:e=>{const t=[];return e.success&&(t.push(`✅ Symbol "${e.symbol}" replaced in ${e.file}.`),t.push("💡 Run invalidate_cache() to refresh the graph after editing."),t.push("💡 Run validate_ctx_contracts() to check if .ctx docs need updating.")),t},get_mode:e=>{const t=[`📋 Current mode: ${e.mode} — ${e.description}`];return 2===e.mode&&t.push("💡 Workflow: get_compressed_file() → read → edit_compressed() → write."),3===e.mode&&t.push("💡 Hybrid workflow: edit compact → validate_pipeline → expand_project → .expanded/ ready for ESLint/tsc."),t},set_mode:e=>e.saved?[`✅ Mode set to ${e.config.mode}. Saved to ${e.path}.`]:[],validate_pipeline:e=>{const t=[`${"PASS"===e.status?"✅":"❌"} Pipeline ${e.status} (${e.duration}): ${e.summary.contractErrors} contract errors, ${e.summary.astErrors} AST errors.`];return"PASS"===e.status&&t.push(`💡 ${e.summary.jsdocInjected} JSDoc blocks injected. Token savings: ${e.summary.tokenSavings}.`),e.summary.contractErrors>0&&t.push("⚠️ Fix .ctx contract errors first, then re-run validate_pipeline."),t},expand_project:e=>[`✅ Expanded ${e.files} files → ${e.outputDir}. ${e.totalJSDocInjected} JSDoc blocks injected.`]},ge={navigate:e=>{const t={expand:"expand",deps:"deps",usages:"usages",call_chain:"get_call_chain",sub_projects:"discover_sub_projects"}[e.action];if(!t)throw new Error(`Unknown navigate action: ${e.action}`);return me[t](e)},analyze:e=>{const t={dead_code:"get_dead_code",similar_functions:"get_similar_functions",complexity:"get_complexity",large_files:"get_large_files",outdated_patterns:"get_outdated_patterns",full_analysis:"get_full_analysis",analysis_summary:"get_analysis_summary",undocumented:"get_undocumented"}[e.action];if(!t)throw new Error(`Unknown analyze action: ${e.action}`);return me[t](e)},testing:e=>{const t={pending:"get_pending_tests",pass:"mark_test_passed",fail:"mark_test_failed",summary:"get_test_summary",reset:"reset_test_state"}[e.action];if(!t)throw new Error(`Unknown testing action: ${e.action}`);return me[t](e)},filters:e=>{const t={get:"get_filters",set:"set_filters",add_excludes:"add_excludes",remove_excludes:"remove_excludes",reset:"reset_filters"}[e.action];if(!t)throw new Error(`Unknown filters action: ${e.action}`);return me[t](e)},jsdoc:e=>{const t={check_consistency:"check_jsdoc_consistency",check_types:"check_types",generate:"generate_jsdoc"}[e.action];if(!t)throw new Error(`Unknown jsdoc action: ${e.action}`);return me[t](e)},docs:e=>{const t={get:"get_project_docs",generate:"generate_context_docs",check_stale:"check_stale_docs",validate_contracts:"validate_ctx_contracts"}[e.action];if(!t)throw new Error(`Unknown docs action: ${e.action}`);return me[t](e)},compact:e=>{const t={compact_file:"get_compressed_file",edit:"edit_compressed",compact_all:"compact_project",beautify:"beautify_project",expand_file:"expand_file",expand_project:"expand_project",validate_pipeline:"validate_pipeline",get_mode:"get_mode",set_mode:"set_mode"}[e.action];if(!t)throw new Error(`Unknown compact action: ${e.action}`);return me[t](e)},db:e=>{const t={schema:"get_db_schema",table_usage:"get_table_usage",dead_tables:"get_db_dead_tables"}[e.action];if(!t)throw new Error(`Unknown db action: ${e.action}`);return me[t](e)}},he={navigate:(e,t)=>{const s=_e[{expand:"expand",deps:"deps",call_chain:"get_call_chain"}[t.action]];return s?s(e):[]},analyze:(e,t)=>{const s=_e[{dead_code:"get_dead_code",full_analysis:"get_full_analysis",complexity:"get_complexity",undocumented:"get_undocumented",similar_functions:"get_similar_functions"}[t.action]];return s?s(e):[]},testing:(e,t)=>"pending"===t.action&&_e.get_pending_tests?.(e)||[],docs:(e,t)=>{const s=_e[{get:"get_project_docs",check_stale:"check_stale_docs",generate:"generate_context_docs",validate_contracts:"validate_ctx_contracts"}[t.action]];return s?s(e):[]},compact:(e,t)=>{const s=_e[{compact_file:"get_compressed_file",edit:"edit_compressed",get_mode:"get_mode",set_mode:"set_mode",validate_pipeline:"validate_pipeline",expand_project:"expand_project"}[t.action]];return s?s(e):[]},db:(e,t)=>{const s=_e[{schema:"get_db_schema",table_usage:"get_table_usage",dead_tables:"get_db_dead_tables"}[t.action]];return s?s(e):[]}};
+const c=t.join(o,n,r),d=t.join(o,".context",n,r);return pe(c)?i=le(c,"utf-8"):pe(d)&&(i=le(d,"utf-8")),se(s,i)},expand_project:e=>oe(A(e.path),{dryRun:e.dryRun||!1}),validate_pipeline:e=>ae(A(e.path),{strict:e.strict||!1})},_e={get_skeleton:()=>['💡 Use expand("SYMBOL") to see code for a specific class.','💡 Use deps("SYMBOL") to see architecture dependencies.',"💡 After code changes, run invalidate_cache() to refresh the graph.","🌐 Web explorer: run `npx project-graph-mcp serve .` to browse code visually."],expand:e=>{const t=[];return e.methods?.length>10&&t.push("💡 Large class detected. Run get_complexity() to find refactoring targets."),t.push("💡 Use deps() to see what depends on this symbol."),e.file&&t.push(`📝 No .ctx for ${e.file}? Run generate_context_docs({ scope: ["${e.file}"] }) to create documentation.`),t},deps:()=>["💡 Use usages() for cross-project reference search."],get_call_chain:e=>e.error?[]:["💡 Use expand() on intermediate steps to understand how data is passed along the chain."],invalidate_cache:()=>["✅ Cache cleared. Run get_skeleton() to rebuild the project graph."],get_dead_code:e=>{const t=["💡 Review each item before removing — some may be used dynamically."];return e.unusedExports?.length>20&&t.push('💡 Consider delegating cleanup to agent-pool: delegate_task({ prompt: "Remove dead code..." })'),t},get_full_analysis:()=>['💡 Focus on items with "critical" severity first.',"💡 Run individual tools (get_complexity, get_dead_code) for detailed breakdowns."],get_complexity:()=>["💡 Functions with complexity >10 are candidates for refactoring.","💡 Use expand() to read the function code before refactoring."],get_undocumented:()=>["💡 Use generate_jsdoc() to auto-generate documentation templates."],get_similar_functions:()=>["💡 Consider extracting duplicated logic into a shared utility."],get_pending_tests:()=>["💡 Use mark_test_passed(testId) or mark_test_failed(testId, reason) to track progress."],get_db_schema:e=>{const t=[];return e.totalTables>0?t.push(`💡 Found ${e.totalTables} tables. Use get_table_usage() to see which code reads/writes them.`):t.push("💡 No .sql schema files found. Add schema.sql or migrations/*.sql to your project."),t},get_table_usage:e=>{const t=["💡 Use get_db_dead_tables() to find tables defined in schema but never queried."];return 0===e.totalTables&&t.push("💡 No SQL queries detected. This tool finds SQL in .query(), .execute(), sql`...` patterns."),t},get_db_dead_tables:()=>["💡 Dead columns detection is best-effort — verify before removing."],get_compressed_file:e=>{const t=[`💡 Saved ${e.savings} tokens (${e.original} → ${e.compressed}).`];return t.push("💡 Use get_ai_context() for full project boot: skeleton + docs + compressed files."),e.file&&t.push(`📝 Working on ${e.file}? Run generate_context_docs({ scope: ["${e.file}"] }) to document it.`),t},get_project_docs:e=>{const t=["💡 Enrich docs by editing .context/*.ctx files — they are git-tracked.","💡 Use generate_context_docs() to create initial .ctx stubs."];return e.staleFiles?.length>0&&t.push(`⚠️ ${e.staleFiles.length} .ctx files are STALE: ${e.staleFiles.slice(0,5).join(", ")}. Run generate_context_docs({ scope: ${JSON.stringify(e.staleFiles)}, overwrite: true }) to update (descriptions will be preserved).`),t},check_stale_docs:e=>{const t=[];return e.stale?.length>0?(t.push(`⚠️ ${e.stale.length} stale: ${e.stale.join(", ")}`),t.push(`💡 Run generate_context_docs({ scope: ${JSON.stringify(e.stale)}, overwrite: true }) — existing descriptions will be preserved.`)):t.push("✅ All .ctx docs are up to date."),e.unknown>0&&t.push(`ℹ️ ${e.unknown} .ctx files without @sig header (pre-staleness format).`),t},generate_context_docs:e=>{const t=[];return e.created?.length>0&&t.push(`✅ Created ${e.created.length} .ctx files with @sig hashes.`),e.skipped?.length>0&&t.push(`ℹ️ Skipped ${e.skipped.length} existing files. Use overwrite=true to regenerate (descriptions are preserved via merge).`),e.templates&&Object.keys(e.templates).length>0&&(t.push("📝 .ctx files have {DESCRIBE} markers. To enrich automatically:"),t.push('   delegate_task({ prompt: "Enrich .context/*.ctx files — replace {DESCRIBE} with compact descriptions", skill: "doc-enricher" })'),t.push("   Or enrich manually: read source files and replace {DESCRIBE} markers with pipe-separated descriptions (max 80 chars).")),t},get_ai_context:e=>{const t=[`💡 Context loaded: ${e.totalTokens} tokens (${e.savings} savings vs ${e.vsOriginal} original).`];return t.push("💡 Use expand() to drill into specific symbols. Use get_compressed_file() for additional files."),t.push("📋 Read .context/*.ctx files for typed signatures and documentation. Check .gemini/AGENTS.md for project-specific rules."),e.staleFiles?.length>0&&t.push(`⚠️ ${e.staleFiles.length} .ctx docs are stale. Run generate_context_docs({ scope: ${JSON.stringify(e.staleFiles)}, overwrite: true }) then delegate_task({ skill: "doc-enricher" }) to update.`),t},validate_ctx_contracts:e=>{const t=[];return e.summary?.errors>0?t.push(`⚠️ ${e.summary.errors} contract violations found. Run generate_context_docs({ overwrite: true }) to regenerate .ctx files.`):t.push("✅ All .ctx contracts valid — documentation matches source."),t},edit_compressed:e=>{const t=[];return e.success&&(t.push(`✅ Symbol "${e.symbol}" replaced in ${e.file}.`),t.push("💡 Run invalidate_cache() to refresh the graph after editing."),t.push("💡 Run validate_ctx_contracts() to check if .ctx docs need updating.")),t},get_mode:e=>{const t=[`📋 Current mode: ${e.mode} — ${e.description}`];return 1===e.mode&&(t.push("💡 Compact mode: read/write .js directly. Run expand_project to update .expanded/ for human review."),t.push("🌐 Web explorer: `npx project-graph-mcp serve .` for visual code browsing with compression stats.")),2===e.mode&&(t.push("💡 Full mode: get_compressed_file() → read → edit_compressed() → write."),t.push("🌐 Web explorer: `npx project-graph-mcp serve .` for visual code browsing with compression stats.")),t},set_mode:e=>e.saved?[`✅ Mode set to ${e.config.mode}. Saved to ${e.path}.`]:[],validate_pipeline:e=>{const t=[`${"PASS"===e.status?"✅":"❌"} Pipeline ${e.status} (${e.duration}): ${e.summary.contractErrors} contract errors, ${e.summary.astErrors} AST errors.`];return"PASS"===e.status&&t.push(`💡 ${e.summary.jsdocInjected} JSDoc blocks injected. Token savings: ${e.summary.tokenSavings}.`),e.summary.contractErrors>0&&t.push("⚠️ Fix .ctx contract errors first, then re-run validate_pipeline."),t},expand_project:e=>[`✅ Expanded ${e.files} files → ${e.outputDir}. ${e.totalJSDocInjected} JSDoc blocks injected.`]},ge={navigate:e=>{const t={expand:"expand",deps:"deps",usages:"usages",call_chain:"get_call_chain",sub_projects:"discover_sub_projects"}[e.action];if(!t)throw new Error(`Unknown navigate action: ${e.action}`);return me[t](e)},analyze:e=>{const t={dead_code:"get_dead_code",similar_functions:"get_similar_functions",complexity:"get_complexity",large_files:"get_large_files",outdated_patterns:"get_outdated_patterns",full_analysis:"get_full_analysis",analysis_summary:"get_analysis_summary",undocumented:"get_undocumented"}[e.action];if(!t)throw new Error(`Unknown analyze action: ${e.action}`);return me[t](e)},testing:e=>{const t={pending:"get_pending_tests",pass:"mark_test_passed",fail:"mark_test_failed",summary:"get_test_summary",reset:"reset_test_state"}[e.action];if(!t)throw new Error(`Unknown testing action: ${e.action}`);return me[t](e)},filters:e=>{const t={get:"get_filters",set:"set_filters",add_excludes:"add_excludes",remove_excludes:"remove_excludes",reset:"reset_filters"}[e.action];if(!t)throw new Error(`Unknown filters action: ${e.action}`);return me[t](e)},jsdoc:e=>{const t={check_consistency:"check_jsdoc_consistency",check_types:"check_types",generate:"generate_jsdoc"}[e.action];if(!t)throw new Error(`Unknown jsdoc action: ${e.action}`);return me[t](e)},docs:e=>{const t={get:"get_project_docs",generate:"generate_context_docs",check_stale:"check_stale_docs",validate_contracts:"validate_ctx_contracts"}[e.action];if(!t)throw new Error(`Unknown docs action: ${e.action}`);return me[t](e)},compact:e=>{const t={compact_file:"get_compressed_file",edit:"edit_compressed",compact_all:"compact_project",beautify:"beautify_project",expand_file:"expand_file",expand_project:"expand_project",validate_pipeline:"validate_pipeline",get_mode:"get_mode",set_mode:"set_mode"}[e.action];if(!t)throw new Error(`Unknown compact action: ${e.action}`);return me[t](e)},db:e=>{const t={schema:"get_db_schema",table_usage:"get_table_usage",dead_tables:"get_db_dead_tables"}[e.action];if(!t)throw new Error(`Unknown db action: ${e.action}`);return me[t](e)}},he={navigate:(e,t)=>{const s=_e[{expand:"expand",deps:"deps",call_chain:"get_call_chain"}[t.action]];return s?s(e):[]},analyze:(e,t)=>{const s=_e[{dead_code:"get_dead_code",full_analysis:"get_full_analysis",complexity:"get_complexity",undocumented:"get_undocumented",similar_functions:"get_similar_functions"}[t.action]];return s?s(e):[]},testing:(e,t)=>"pending"===t.action&&_e.get_pending_tests?.(e)||[],docs:(e,t)=>{const s=_e[{get:"get_project_docs",check_stale:"check_stale_docs",generate:"generate_context_docs",validate_contracts:"validate_ctx_contracts"}[t.action]];return s?s(e):[]},compact:(e,t)=>{const s=_e[{compact_file:"get_compressed_file",edit:"edit_compressed",get_mode:"get_mode",set_mode:"set_mode",validate_pipeline:"validate_pipeline",expand_project:"expand_project"}[t.action]];return s?s(e):[]},db:(e,t)=>{const s=_e[{schema:"get_db_schema",table_usage:"get_table_usage",dead_tables:"get_db_dead_tables"}[t.action]];return s?s(e):[]}};
 export function createServer(s){let n=1;
 const i=new Map;
-let c=!1;return{pendingRequests:i,async handleMessage(s){if(void 0!==s.result||void 0!==s.error){const e=i.get(s.id);return e&&(i.delete(s.id),s.error?e.reject(new Error(s.error.message)):e.resolve(s.result)),null}const{method:a,params:r,id:n}=s;if(void 0===n)return await this.handleNotification(a,r),null;try{switch(a){case"initialize":return r?.capabilities?.roots&&(c=!0),r?.roots&&q(r.roots),{jsonrpc:"2.0",id:n,result:{protocolVersion:"2024-11-05",capabilities:{tools:{},resources:{}},serverInfo:{name:"project-graph",version:"2.0.0"}}};case"resources/list":return{jsonrpc:"2.0",id:n,result:{resources:[{uri:"project-graph://guide",name:"Project Graph Usage Guide",description:"Comprehensive guide with workflows and examples",mimeType:"text/markdown"}]}};case"resources/read":return"project-graph://guide"!==r.uri?{jsonrpc:"2.0",id:n,error:{code:-32602,message:`Resource not found: ${r.uri}`}}:{jsonrpc:"2.0",id:n,result:{contents:[{uri:"project-graph://guide",mimeType:"text/markdown",text:e.readFileSync(t.join(ue,"..","..","GUIDE.md"),"utf8")}]}};case"tools/list":return{jsonrpc:"2.0",id:n,result:{tools:o}};case"tools/call":{const e=await this.executeTool(r.name,r.arguments),t=[{type:"text",text:JSON.stringify(e,null,2)}];
+let c=!1;return{pendingRequests:i,async handleMessage(s){if(void 0!==s.result||void 0!==s.error){const e=i.get(s.id);return e&&(i.delete(s.id),s.error?e.reject(new Error(s.error.message)):e.resolve(s.result)),null}const{method:a,params:r,id:n}=s;if(void 0===n)return await this.handleNotification(a,r),null;try{switch(a){case"initialize":return r?.capabilities?.roots&&(c=!0),r?.roots&&q(r.roots),{jsonrpc:"2.0",id:n,result:{protocolVersion:"2024-11-05",capabilities:{tools:{},resources:{}},serverInfo:{name:"project-graph",version:"2.1.0"}}};case"resources/list":return{jsonrpc:"2.0",id:n,result:{resources:[{uri:"project-graph://guide",name:"Project Graph Usage Guide",description:"Comprehensive guide with workflows and examples",mimeType:"text/markdown"}]}};case"resources/read":return"project-graph://guide"!==r.uri?{jsonrpc:"2.0",id:n,error:{code:-32602,message:`Resource not found: ${r.uri}`}}:{jsonrpc:"2.0",id:n,result:{contents:[{uri:"project-graph://guide",mimeType:"text/markdown",text:e.readFileSync(t.join(ue,"..","..","GUIDE.md"),"utf8")}]}};case"tools/list":return{jsonrpc:"2.0",id:n,result:{tools:o}};case"tools/call":{const e=await this.executeTool(r.name,r.arguments),t=[{type:"text",text:JSON.stringify(e,null,2)}];
 let s=[];
 const o=he[r.name];if(o&&r.arguments?.action)s=o(e,r.arguments);else{const t=_e[r.name];t&&(s=t(e))}return s.length>0&&t.push({type:"text",text:"\n"+s.join("\n")}),{jsonrpc:"2.0",id:n,result:{content:t}}}default:return{jsonrpc:"2.0",id:n,error:{code:-32601,message:`Method not found: ${a}`}}}}catch(e){return{jsonrpc:"2.0",id:n,error:{code:-32e3,message:e.message}}}},async handleNotification(e,t){switch(e){case"notifications/initialized":if(c)try{const e=await this.requestRoots();e&&e.length>0&&q(e)}catch(e){console.error(`[project-graph] Failed to get roots: ${e.message}`)}break;case"notifications/roots/list_changed":if(c)try{const e=await this.requestRoots();e&&e.length>0&&(q(e),p())}catch(e){console.error(`[project-graph] Failed to refresh roots: ${e.message}`)}}},requestRoots:()=>new Promise((e,t)=>{const o=n++,a=setTimeout(()=>{i.delete(o),t(new Error("roots/list request timed out"))},5e3);i.set(o,{resolve:t=>{clearTimeout(a),e(t.roots||[])},reject:e=>{clearTimeout(a),t(e)}}),s({jsonrpc:"2.0",id:o,method:"roots/list"})}),async executeTool(e,t){a(e,t);
 const s=Date.now();try{const o=ge[e];

package/src/mcp/tool-defs.js

@@ -1,3 +1,3 @@
 // @ctx .context/src/mcp/tool-defs.ctx
 const e={get_skeleton:{name:"get_skeleton",description:"Get compact minified project overview (10-50x smaller than source). Returns legend, stats, and node summaries.",inputSchema:{type:"object",properties:{path:{type:"string",description:'Path to scan (e.g., "src/components")'}},required:["path"]}},get_focus_zone:{name:"get_focus_zone",description:"Get enriched context for recently modified files. Auto-detects from git or accepts explicit file list.",inputSchema:{type:"object",properties:{path:{type:"string"},useGitDiff:{type:"boolean",description:"Auto-detect from git diff"},recentFiles:{type:"array",items:{type:"string"},description:"Explicit list of files to expand"}}}},get_ai_context:{name:"get_ai_context",description:"Boot AI agent context: skeleton + doc-dialect + optional compressed files in one call. Call FIRST when starting work on a new project. Returns totalTokens and savings vs reading raw source.",inputSchema:{type:"object",properties:{path:{type:"string",description:"Project root path"},includeFiles:{type:"array",items:{type:"string"},description:'Specific files to include compressed (e.g., ["parser.js", "tools.js"])'},includeDocs:{type:"boolean",description:"Include doc-dialect documentation (default: true)"},includeSkeleton:{type:"boolean",description:"Include project skeleton (default: true)"}},required:["path"]}},invalidate_cache:{name:"invalidate_cache",description:"Invalidate the cached graph. Use after making code changes.",inputSchema:{type:"object",properties:{}}},get_usage_guide:{name:"get_usage_guide",description:"Get the comprehensive usage guide for project-graph with examples and best practices.\nCall this FIRST when planning how to analyze, navigate, or audit a codebase.\nReturns practical examples and recommended workflow for each feature area.\n\nAvailable topics: navigation, analysis, testing, documentation, rules, workflow.\nOmit topic to get the full guide.",inputSchema:{type:"object",properties:{topic:{type:"string",description:"Optional topic filter: navigation, analysis, testing, documentation, rules, workflow"}}}},get_agent_instructions:{name:"get_agent_instructions",description:"Get coding guidelines, architectural standards, and JSDoc rules for this project.",inputSchema:{type:"object",properties:{}}},get_custom_rules:{name:"get_custom_rules",description:"List all custom code analysis rules. Rules are stored in JSON files in rules/ directory.",inputSchema:{type:"object",properties:{}}},set_custom_rule:{name:"set_custom_rule",description:"Add or update a custom code analysis rule. Creates ruleset if it does not exist.",inputSchema:{type:"object",properties:{ruleSet:{type:"string",description:'Name of ruleset (e.g., "symbiote", "react", "custom")'},rule:{type:"object",description:"Rule definition with id, name, description, pattern, patternType, replacement, severity, filePattern"}},required:["ruleSet","rule"]}},check_custom_rules:{name:"check_custom_rules",description:"Run custom rules analysis on a directory. Returns violations found.",inputSchema:{type:"object",properties:{path:{type:"string",description:"Path to scan"},ruleSet:{type:"string",description:"Optional: specific ruleset to use"},severity:{type:"string",description:"Optional: filter by severity (error/warning/info)"}},required:["path"]}},get_framework_reference:{name:"get_framework_reference",description:"Get framework-specific AI reference documentation. Auto-detects framework from project or accepts explicit name. Returns full API reference, patterns, and common mistakes as agent context.",inputSchema:{type:"object",properties:{framework:{type:"string",description:'Framework reference name (e.g., "symbiote-3x"). If omitted, auto-detects from path.'},path:{type:"string",description:'Project path for auto-detection (e.g., "src/")'}}}}};
-export const TOOLS=[e.get_skeleton,e.get_focus_zone,e.get_ai_context,e.invalidate_cache,e.get_usage_guide,e.get_agent_instructions,e.get_custom_rules,e.set_custom_rule,e.check_custom_rules,e.get_framework_reference,{name:"navigate",description:"Navigate the project graph. Actions: expand|deps|usages|call_chain|sub_projects",inputSchema:{type:"object",properties:{action:{type:"string",enum:["expand","deps","usages","call_chain","sub_projects"],description:"Navigation action to perform"},symbol:{type:"string",description:"Symbol name (for expand, deps, usages)"},from:{type:"string",description:"Starting symbol (for call_chain)"},to:{type:"string",description:"Target symbol (for call_chain)"},path:{type:"string",description:"Path to scan (for call_chain, sub_projects)"}},required:["action"]}},{name:"analyze",description:"Code quality analysis. Actions: dead_code|similar_functions|complexity|large_files|outdated_patterns|full_analysis|analysis_summary|undocumented",inputSchema:{type:"object",properties:{action:{type:"string",enum:["dead_code","similar_functions","complexity","large_files","outdated_patterns","full_analysis","analysis_summary","undocumented"],description:"Analysis type to run"},path:{type:"string",description:"Path to scan"},minComplexity:{type:"number",description:"For complexity: minimum threshold (default: 1)"},onlyProblematic:{type:"boolean",description:"For complexity/large_files: only show issues"},threshold:{type:"number",description:"For similar_functions: min similarity % (default: 60)"},includeItems:{type:"boolean",description:"For full_analysis: include individual items"},level:{type:"string",enum:["tests","params","all"],description:"For undocumented: strictness level"},codeOnly:{type:"boolean",description:"For outdated_patterns: only check code"},depsOnly:{type:"boolean",description:"For outdated_patterns: only check deps"}},required:["action","path"]}},{name:"testing",description:"Test checklist management. Actions: pending|pass|fail|summary|reset",inputSchema:{type:"object",properties:{action:{type:"string",enum:["pending","pass","fail","summary","reset"],description:"Test action to perform"},path:{type:"string",description:"Path to scan (for pending, summary)"},testId:{type:"string",description:"Test ID (for pass, fail)"},reason:{type:"string",description:"Failure reason (for fail)"}},required:["action"]}},{name:"filters",description:"Filter configuration. Actions: get|set|add_excludes|remove_excludes|reset",inputSchema:{type:"object",properties:{action:{type:"string",enum:["get","set","add_excludes","remove_excludes","reset"],description:"Filter action to perform"},excludeDirs:{type:"array",items:{type:"string"},description:"For set: directories to exclude"},excludePatterns:{type:"array",items:{type:"string"},description:"For set: file patterns to exclude"},useGitignore:{type:"boolean",description:"For set: use .gitignore patterns"},includeHidden:{type:"boolean",description:"For set: include hidden directories"},dirs:{type:"array",items:{type:"string"},description:"For add_excludes/remove_excludes"}},required:["action"]}},{name:"jsdoc",description:"JSDoc operations. Actions: check_consistency|check_types|generate",inputSchema:{type:"object",properties:{action:{type:"string",enum:["check_consistency","check_types","generate"],description:"JSDoc action to perform"},path:{type:"string",description:"Path to scan"},name:{type:"string",description:"For generate: specific function name"},files:{type:"array",items:{type:"string"},description:"For check_types: specific files"},maxDiagnostics:{type:"number",description:"For check_types: max diagnostics (default: 50)"}},required:["action","path"]}},{name:"docs",description:"Documentation (.ctx) management. Actions: get|generate|check_stale|validate_contracts",inputSchema:{type:"object",properties:{action:{type:"string",enum:["get","generate","check_stale","validate_contracts"],description:"Documentation action to perform"},path:{type:"string",description:"Project root path"},file:{type:"string",description:"For get: specific file docs"},overwrite:{type:"boolean",description:"For generate: overwrite existing (merge preserves descriptions)"},scope:{description:'For generate: "all", "focus" (git diff), or array of file paths'},strict:{type:"boolean",description:"For validate_contracts: report functions missing from .ctx"}},required:["action","path"]}},{name:"compact",description:"Compact code operations. Actions: compact_file|edit|compact_all|beautify|expand_file|expand_project|validate_pipeline|get_mode|set_mode",inputSchema:{type:"object",properties:{action:{type:"string",enum:["compact_file","edit","compact_all","beautify","expand_file","expand_project","validate_pipeline","get_mode","set_mode"],description:"Compact action to perform"},path:{type:"string",description:"Path to file or directory"},symbol:{type:"string",description:"For edit: function/class name to replace"},code:{type:"string",description:"For edit: new code for the symbol"},beautify:{type:"boolean",description:"Beautify output (default: true)"},legend:{type:"boolean",description:"For compact_file: include export legend"},dryRun:{type:"boolean",description:"Preview without modifying"},mode:{type:"number",description:"For set_mode: mode number 1, 2, 3, or 4"},autoValidate:{type:"boolean",description:"For set_mode: auto-validate after edits"},stripJSDoc:{type:"boolean",description:"For set_mode: strip JSDoc when compacting"},strict:{type:"boolean",description:"For validate_pipeline: report fns missing from .ctx"}},required:["action"]}},{name:"db",description:"Database analysis. Actions: schema|table_usage|dead_tables",inputSchema:{type:"object",properties:{action:{type:"string",enum:["schema","table_usage","dead_tables"],description:"Database analysis action"},path:{type:"string",description:"Path to scan"},table:{type:"string",description:"For table_usage: filter to specific table"}},required:["action","path"]}}];
+export const TOOLS=[e.get_skeleton,e.get_focus_zone,e.get_ai_context,e.invalidate_cache,e.get_usage_guide,e.get_agent_instructions,e.get_custom_rules,e.set_custom_rule,e.check_custom_rules,e.get_framework_reference,{name:"navigate",description:"Navigate the project graph. Actions: expand|deps|usages|call_chain|sub_projects",inputSchema:{type:"object",properties:{action:{type:"string",enum:["expand","deps","usages","call_chain","sub_projects"],description:"Navigation action to perform"},symbol:{type:"string",description:"Symbol name (for expand, deps, usages)"},from:{type:"string",description:"Starting symbol (for call_chain)"},to:{type:"string",description:"Target symbol (for call_chain)"},path:{type:"string",description:"Path to scan (for call_chain, sub_projects)"}},required:["action"]}},{name:"analyze",description:"Code quality analysis. Actions: dead_code|similar_functions|complexity|large_files|outdated_patterns|full_analysis|analysis_summary|undocumented",inputSchema:{type:"object",properties:{action:{type:"string",enum:["dead_code","similar_functions","complexity","large_files","outdated_patterns","full_analysis","analysis_summary","undocumented"],description:"Analysis type to run"},path:{type:"string",description:"Path to scan"},minComplexity:{type:"number",description:"For complexity: minimum threshold (default: 1)"},onlyProblematic:{type:"boolean",description:"For complexity/large_files: only show issues"},threshold:{type:"number",description:"For similar_functions: min similarity % (default: 60)"},includeItems:{type:"boolean",description:"For full_analysis: include individual items"},level:{type:"string",enum:["tests","params","all"],description:"For undocumented: strictness level"},codeOnly:{type:"boolean",description:"For outdated_patterns: only check code"},depsOnly:{type:"boolean",description:"For outdated_patterns: only check deps"}},required:["action","path"]}},{name:"testing",description:"Test checklist management. Actions: pending|pass|fail|summary|reset",inputSchema:{type:"object",properties:{action:{type:"string",enum:["pending","pass","fail","summary","reset"],description:"Test action to perform"},path:{type:"string",description:"Path to scan (for pending, summary)"},testId:{type:"string",description:"Test ID (for pass, fail)"},reason:{type:"string",description:"Failure reason (for fail)"}},required:["action"]}},{name:"filters",description:"Filter configuration. Actions: get|set|add_excludes|remove_excludes|reset",inputSchema:{type:"object",properties:{action:{type:"string",enum:["get","set","add_excludes","remove_excludes","reset"],description:"Filter action to perform"},excludeDirs:{type:"array",items:{type:"string"},description:"For set: directories to exclude"},excludePatterns:{type:"array",items:{type:"string"},description:"For set: file patterns to exclude"},useGitignore:{type:"boolean",description:"For set: use .gitignore patterns"},includeHidden:{type:"boolean",description:"For set: include hidden directories"},dirs:{type:"array",items:{type:"string"},description:"For add_excludes/remove_excludes"}},required:["action"]}},{name:"jsdoc",description:"JSDoc operations. Actions: check_consistency|check_types|generate",inputSchema:{type:"object",properties:{action:{type:"string",enum:["check_consistency","check_types","generate"],description:"JSDoc action to perform"},path:{type:"string",description:"Path to scan"},name:{type:"string",description:"For generate: specific function name"},files:{type:"array",items:{type:"string"},description:"For check_types: specific files"},maxDiagnostics:{type:"number",description:"For check_types: max diagnostics (default: 50)"}},required:["action","path"]}},{name:"docs",description:"Documentation (.ctx) management. Actions: get|generate|check_stale|validate_contracts",inputSchema:{type:"object",properties:{action:{type:"string",enum:["get","generate","check_stale","validate_contracts"],description:"Documentation action to perform"},path:{type:"string",description:"Project root path"},file:{type:"string",description:"For get: specific file docs"},overwrite:{type:"boolean",description:"For generate: overwrite existing (merge preserves descriptions)"},scope:{description:'For generate: "all", "focus" (git diff), or array of file paths'},strict:{type:"boolean",description:"For validate_contracts: report functions missing from .ctx"}},required:["action","path"]}},{name:"compact",description:"Compact code operations. Actions: compact_file|edit|compact_all|beautify|expand_file|expand_project|validate_pipeline|get_mode|set_mode",inputSchema:{type:"object",properties:{action:{type:"string",enum:["compact_file","edit","compact_all","beautify","expand_file","expand_project","validate_pipeline","get_mode","set_mode"],description:"Compact action to perform"},path:{type:"string",description:"Path to file or directory"},symbol:{type:"string",description:"For edit: function/class name to replace"},code:{type:"string",description:"For edit: new code for the symbol"},beautify:{type:"boolean",description:"Beautify output (default: true)"},legend:{type:"boolean",description:"For compact_file: include export legend"},dryRun:{type:"boolean",description:"Preview without modifying"},mode:{type:"number",description:"For set_mode: 1 (compact, recommended) or 2 (full)"},autoValidate:{type:"boolean",description:"For set_mode: auto-validate after edits"},stripJSDoc:{type:"boolean",description:"For set_mode: strip JSDoc when compacting"},strict:{type:"boolean",description:"For validate_pipeline: report fns missing from .ctx"}},required:["action"]}},{name:"db",description:"Database analysis. Actions: schema|table_usage|dead_tables",inputSchema:{type:"object",properties:{action:{type:"string",enum:["schema","table_usage","dead_tables"],description:"Database analysis action"},path:{type:"string",description:"Path to scan"},table:{type:"string",description:"For table_usage: filter to specific table"}},required:["action","path"]}}];

package/web/app.js

@@ -13,4 +13,5 @@ async function f(){g(),l(),i("project",t=>{t&&(document.title=`${t.name} — Pro
 const n=new Set;for(const o of Object.values(t.n||{}))o.f&&n.add(o.f);for(const o of Object.keys(t.X||{}))n.add(o);for(const[o,a]of Object.entries(t.f||{}))for(const t of a)n.add("./"===o?t:`${o}${t}`);for(const[o,a]of Object.entries(t.a||{}))for(const t of a)n.add("./"===o?t:`${o}${t}`);
 const o=document.getElementById("project-files");o&&(o.textContent=`${n.size} files`),emit("skeleton-loaded",t),fetch(m+"api/compression-stats").then(t=>t.json()).then(t=>{const n=document.getElementById("compression-stats");if(n&&t.codeTok){const o=t.ctxTok?`${(t.codeTok/1e3).toFixed(1)}K + ${(t.ctxTok/1e3).toFixed(1)}K ctx = ${(t.totalTok/1e3).toFixed(1)}K tok`:`${(t.codeTok/1e3).toFixed(1)}K tok`;n.textContent=o,n.style.display=""}})}),i("connected",t=>{const n=document.getElementById("status-indicator");n&&(n.className=t?"status connected":"status disconnected")}),r(t=>{if("agent_connect"===t.type||"agent_disconnect"===t.type)return h(t.agents),void emit("agent-event",t);state.monitorEvents.push(t),state.monitorEvents.length>500&&state.monitorEvents.shift(),emit("tool-event",t)})}
 function h(t){let n=document.getElementById("agent-badge");if(!n){const t=document.querySelector(".app-topbar");if(!t)return;n=document.createElement("span"),n.id="agent-badge",n.className="agent-badge",t.appendChild(n)}n.textContent=t>0?`● ${t} agent${1!==t?"s":""}`:"",n.style.display=t>0?"":"none"}
-function y(){document.querySelector("pg-quick-open")||document.body.appendChild(document.createElement("pg-quick-open"))}"loading"===document.readyState?document.addEventListener("DOMContentLoaded",()=>{f(),y()}):setTimeout(()=>{f(),y()},100);
+function y(){document.querySelector("pg-quick-open")||document.body.appendChild(document.createElement("pg-quick-open"))}
+"loading"===document.readyState?document.addEventListener("DOMContentLoaded",()=>{f(),y()}):setTimeout(()=>{f(),y()},100);