kirograph 0.15.0 → 0.16.1

package/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Davide De Sio
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

@@ -82,7 +82,7 @@ See the [Architecture Analysis](#architecture-analysis-opt-in-1) section below f
 
 ### Memory (opt-in)
 
-When `enableMemory: true` is set, KiroGraph stores persistent observations across sessions — decisions, errors, patterns, and architecture notes. Observations are:
+When `enableMemory: true` is set, KiroGraph stores persistent observations across sessions — decisions, errors, patterns, and architecture notes. Inspired by [cavemem](https://github.com/JuliusBrussee/cavemem) by [Julius Brussee](https://www.linkedin.com/in/julius-brussee/). Observations are:
 
 - **Compressed** with the caveman grammar (if caveman mode is enabled) — deterministic, no LLM tokens spent
 - **Linked to code symbols** — identifiers in observation text are matched against the graph and stored as stable `qualified_name` references
@@ -103,6 +103,26 @@ Enable via `kirograph install` or directly in `.kirograph/config.json`:
 
 See the [Memory](#memory-requires-enablememory-true) section below for full details.
 
+### Documentation indexing (opt-in)
+
+When `enableDocs: true` is set, KiroGraph indexes project documentation by heading hierarchy and section structure. Instead of reading entire doc files, agents retrieve exactly the section they need via stable section IDs. Inspired by [jDocMunch-MCP](https://github.com/jgravelle/jdocmunch-mcp) by [J. Gravelle](https://www.linkedin.com/in/j-gravelle-2778223/).
+
+- **9 format parsers**: Markdown, MDX, reStructuredText, AsciiDoc, RDoc, Org-mode, HTML, plain text, OpenAPI/Swagger
+- **Code ↔ docs cross-references**: Backtick references, CamelCase identifiers, and snake_case patterns in docs are resolved against the code graph
+- **Section-level FTS search**: Independent from code search (`kirograph_docs_search`)
+- **Stable section IDs**: `{file_path}::{ancestor-chain/slug}#{level}` — stable across re-indexing
+- **Token savings**: 92–97% reduction vs reading full doc files (tracked in `kirograph_gain`)
+
+Enable via `kirograph install` or directly in `.kirograph/config.json`:
+
+```json
+{
+  "enableDocs": true
+}
+```
+
+See the [Documentation](#documentation-requires-enabledocs-true) section below for full details.
+
 ## Installation
 
 ### From npm (not yet available on npm registry)
@@ -597,6 +617,56 @@ Memory subsystem health: session count, observations, embedding coverage, model
 |-----------|------|---------|-------------|
 | `projectPath` | string | cwd | Project root path |
 
+### `kirograph_docs_toc` *(requires `enableDocs: true`)*
+
+Get table of contents for a documentation file or the whole project. Returns section IDs, titles, levels, and summaries.
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `file` | string | - | Filter to a specific doc file (relative path). Omit for project-wide TOC. |
+| `tree` | boolean | false | Return nested tree structure |
+| `projectPath` | string | cwd | Project root path |
+
+### `kirograph_docs_search` *(requires `enableDocs: true`)*
+
+Search documentation sections by query. Returns matching sections ranked by relevance. Independent from `kirograph_search` (code-only).
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `query` | string | required | Search query (natural language or keywords) |
+| `file` | string | - | Narrow search to a specific doc file |
+| `limit` | number | 10 | Max results |
+| `projectPath` | string | cwd | Project root path |
+
+### `kirograph_docs_section` *(requires `enableDocs: true`)*
+
+Retrieve full content of a documentation section by its stable ID. Use `context=true` to also get ancestor headings and child summaries.
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `id` | string | required | Section ID (from `kirograph_docs_toc` or `kirograph_docs_search` results) |
+| `context` | boolean | false | Include ancestor heading chain and child summaries |
+| `projectPath` | string | cwd | Project root path |
+
+### `kirograph_docs_outline` *(requires `enableDocs: true`)*
+
+Get the heading hierarchy for a single documentation file. Lighter than full TOC when you know which file is relevant.
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `file` | string | required | Relative path to the doc file |
+| `projectPath` | string | cwd | Project root path |
+
+### `kirograph_docs_refs` *(requires `enableDocs: true`)*
+
+Find code symbols referenced by a doc section, or doc sections that reference a code symbol. Bidirectional lookup.
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `sectionId` | string | - | Doc section ID (find code symbols it references) |
+| `nodeId` | string | - | Code symbol qualified name (find doc sections that reference it) |
+| `projectPath` | string | cwd | Project root path |
+
 ## CLI Reference
 
 ### Setup
@@ -725,6 +795,8 @@ Caveman mode never touches code blocks, file paths, URLs, or technical terms, on
 
 ### Shell Compression (`kirograph_exec`)
 
+![KiroGraph caveman](https://raw.githubusercontent.com/davide-desio-eleva/kirograph/main/assets/rtk.png)
+
 KiroGraph includes a built-in shell compression engine inspired by [rtk](https://github.com/rtk-ai/rtk). The `kirograph_exec` MCP tool runs shell commands and returns token-optimized output, saving 60-90% of tokens on verbose commands like git, test runners, linters, and build tools.
 
 **Why it's useful:** LLM context is expensive. A raw `git status` might be 2,000 tokens; compressed it's 200. A passing test suite might be 25,000 tokens of noise; compressed it's a single "PASSED: 42/42 tests" line. The compression engine knows how to extract the signal from each command family.
@@ -1038,6 +1110,42 @@ kirograph mem lint --fix                  # auto-repair issues
 
 **How observations surface:** `kirograph_context` and `kirograph_impact` automatically include relevant memory observations (max 3, above relevance threshold 0.3) when memory is enabled. No extra tool call needed.
 
+### Documentation *(requires `enableDocs: true`)*
+
+Section-level documentation navigation — search, browse, and retrieve doc sections from the CLI.
+
+```bash
+# Table of contents
+kirograph docs toc                          # whole project
+kirograph docs toc README.md                # single file
+kirograph docs toc README.md --tree         # nested tree structure
+kirograph docs toc --json                   # JSON output
+
+# Search (mirrors kirograph_docs_search)
+kirograph docs search "authentication"
+kirograph docs search "config" --file docs/guide.md
+kirograph docs search "install" --limit 5
+
+# Retrieve a section (mirrors kirograph_docs_section)
+kirograph docs section "README.md::installation#1"
+kirograph docs section "README.md::installation#1" --context
+
+# Outline (mirrors kirograph_docs_outline)
+kirograph docs outline docs/api.md
+
+# Cross-references (mirrors kirograph_docs_refs)
+kirograph docs refs "docs/auth.md::oauth/token-refresh#2"
+
+# Maintenance
+kirograph docs reindex                      # force full re-index
+kirograph docs lint                         # health checks (broken refs, stale sections)
+kirograph docs reembed                      # re-embed with current model
+```
+
+**How sections are identified:** Each section gets a stable ID in the format `{file_path}::{ancestor-chain/slug}#{level}`. IDs remain stable across re-indexing as long as the file path, heading text, heading level, and parent chain don't change.
+
+**How code linking works:** When `docsLinkCode: true` (default), the indexer scans section content for backtick references (`` `functionName` ``), CamelCase identifiers, and snake_case patterns, then resolves them against the code graph. Matches are stored as `doc_code_refs` using `qualified_name` (stable across reindex).
+
 ### Graph Export
 
 Export the full graph as an interactive dashboard. three files served from a local directory, no server required, works offline.
@@ -1556,6 +1664,11 @@ Detected frameworks are stored in config and used to improve symbol extraction a
 
 KiroGraph is inspired by [CodeGraph](https://github.com/colbymchenry/codegraph) by [Colby McHenry](https://www.linkedin.com/in/colby-mchenry/). the original concept of building a semantic code graph for AI coding agents comes from his work.
 
+### Inspirations
+
+- [cavemem](https://github.com/JuliusBrussee/cavemem) by [Julius Brussee](https://www.linkedin.com/in/julius-brussee/): the memory module's hook-based observation capture, deterministic compression, and SQLite storage pattern.
+- [jDocMunch-MCP](https://github.com/jgravelle/jdocmunch-mcp) by [J. Gravelle](https://www.linkedin.com/in/j-gravelle-2778223/): the documentation module's section-first retrieval approach, stable section IDs, and byte-offset addressing.
+
 ### Contributors
 
 - [Alessandro Franceschi](https://www.linkedin.com/in/alessandrofranceschi/). Claude Code and Codex integration, Elixir/Phoenix language and framework support.

package/dist/bin/commands/docs.js

@@ -0,0 +1,357 @@
+"use strict";
+var __defProp = Object.defineProperty;
+var __getOwnPropDesc = Object.getOwnPropertyDescriptor;
+var __getOwnPropNames = Object.getOwnPropertyNames;
+var __hasOwnProp = Object.prototype.hasOwnProperty;
+var __export = (target, all) => {
+  for (var name in all)
+    __defProp(target, name, { get: all[name], enumerable: true });
+};
+var __copyProps = (to, from, except, desc) => {
+  if (from && typeof from === "object" || typeof from === "function") {
+    for (let key of __getOwnPropNames(from))
+      if (!__hasOwnProp.call(to, key) && key !== except)
+        __defProp(to, key, { get: () => from[key], enumerable: !(desc = __getOwnPropDesc(from, key)) || desc.enumerable });
+  }
+  return to;
+};
+var __toCommonJS = (mod) => __copyProps(__defProp({}, "__esModule", { value: true }), mod);
+var docs_exports = {};
+__export(docs_exports, {
+  register: () => register
+});
+module.exports = __toCommonJS(docs_exports);
+var import_config = require("../../config");
+var import_ui = require("../ui");
+function safeCloseAndExit(cg, code = 0) {
+  try {
+    cg.close();
+  } catch {
+  }
+  try {
+    const fs = require("fs");
+    if (process.stdout.writableEnded === false) process.stdout.write("");
+    if (process.stderr.writableEnded === false) process.stderr.write("");
+    fs.closeSync(2);
+    fs.closeSync(1);
+  } catch {
+  }
+  process.exit(code);
+}
+function register(program) {
+  const docs = program.command("docs").description("Documentation navigation (requires enableDocs: true)");
+  docs.command("toc [file]").description("Print table of contents for a file or the whole project").option("--tree", "Show nested tree structure").option("--json", "Output as JSON").action(async (file, opts) => {
+    const cwd = process.cwd();
+    const config = await (0, import_config.loadConfig)(cwd);
+    if (!config.enableDocs) {
+      console.error(`  \u2716 Documentation indexing is not enabled. Set ${import_ui.violet}${import_ui.bold}enableDocs: true${import_ui.reset} in .kirograph/config.json`);
+      console.error(`  ${import_ui.dim}Then re-run:${import_ui.reset} ${import_ui.violet}${import_ui.bold}kirograph index${import_ui.reset}`);
+      process.exit(1);
+    }
+    const KiroGraph = (await Promise.resolve().then(() => require("../../index.js"))).default;
+    if (!KiroGraph.isInitialized(cwd)) {
+      console.error("  \u2716 KiroGraph not initialized. Run: kirograph init");
+      process.exit(1);
+    }
+    const cg = await KiroGraph.open(cwd);
+    const db = cg.getDatabase();
+    db.applyDocsSchema();
+    const { DocsQueries } = await Promise.resolve().then(() => require("../../docs/queries.js"));
+    const queries = new DocsQueries(db.getRawDb(), cwd);
+    const toc = queries.getToc({ file, tree: opts.tree });
+    if (toc.length === 0) {
+      console.log(`  ${import_ui.dim}No documentation sections found.${import_ui.reset} Run ${import_ui.violet}${import_ui.bold}kirograph index${import_ui.reset} first.`);
+      cg.close();
+      return;
+    }
+    if (opts.json) {
+      console.log(JSON.stringify(toc, null, 2));
+    } else {
+      for (const entry of toc) {
+        const prefix = "#".repeat(entry.level || 1);
+        const summary = entry.summary ? ` ${import_ui.dim}\u2014 ${entry.summary}${import_ui.reset}` : "";
+        console.log(`  ${prefix} ${import_ui.bold}${entry.title}${import_ui.reset}${summary}`);
+        console.log(`    ${import_ui.dim}${entry.id}${import_ui.reset}`);
+      }
+    }
+    cg.close();
+  });
+  docs.command("search <query>").description("Search documentation sections").option("--file <path>", "Narrow search to a specific file").option("--limit <n>", "Max results", "10").option("--json", "Output as JSON").action(async (query, opts) => {
+    const cwd = process.cwd();
+    const config = await (0, import_config.loadConfig)(cwd);
+    if (!config.enableDocs) {
+      console.error(`  \u2716 Documentation indexing is not enabled. Set ${import_ui.violet}${import_ui.bold}enableDocs: true${import_ui.reset} in .kirograph/config.json`);
+      process.exit(1);
+    }
+    const KiroGraph = (await Promise.resolve().then(() => require("../../index.js"))).default;
+    if (!KiroGraph.isInitialized(cwd)) {
+      console.error("  \u2716 KiroGraph not initialized.");
+      process.exit(1);
+    }
+    const cg = await KiroGraph.open(cwd);
+    const db = cg.getDatabase();
+    db.applyDocsSchema();
+    const { DocsQueries } = await Promise.resolve().then(() => require("../../docs/queries.js"));
+    const queries = new DocsQueries(db.getRawDb(), cwd, config);
+    const results = await queries.searchSections(query, { file: opts.file, limit: parseInt(opts.limit ?? "10", 10) });
+    if (results.length === 0) {
+      console.log(`  ${import_ui.dim}No sections found matching "${query}".${import_ui.reset}`);
+      cg.close();
+      return;
+    }
+    if (opts.json) {
+      console.log(JSON.stringify(results, null, 2));
+    } else {
+      for (const r of results) {
+        const summary = r.section.summary ? `
+    ${import_ui.dim}${r.section.summary}${import_ui.reset}` : "";
+        console.log(`  ${import_ui.green}\u25CF${import_ui.reset} ${import_ui.bold}${r.section.title}${import_ui.reset} ${import_ui.dim}[${r.section.filePath}]${import_ui.reset}${summary}`);
+        console.log(`    ${import_ui.dim}ID: ${r.section.id}${import_ui.reset}`);
+      }
+    }
+    cg.close();
+  });
+  docs.command("section <id>").description("Print full content of a section by ID").option("--context", "Include ancestor headings and child summaries").action(async (id, opts) => {
+    const cwd = process.cwd();
+    const config = await (0, import_config.loadConfig)(cwd);
+    if (!config.enableDocs) {
+      console.error(`  \u2716 Documentation indexing is not enabled. Set ${import_ui.violet}${import_ui.bold}enableDocs: true${import_ui.reset} in .kirograph/config.json`);
+      process.exit(1);
+    }
+    const KiroGraph = (await Promise.resolve().then(() => require("../../index.js"))).default;
+    if (!KiroGraph.isInitialized(cwd)) {
+      console.error("  \u2716 KiroGraph not initialized.");
+      process.exit(1);
+    }
+    const cg = await KiroGraph.open(cwd);
+    const db = cg.getDatabase();
+    db.applyDocsSchema();
+    const { DocsQueries } = await Promise.resolve().then(() => require("../../docs/queries.js"));
+    const queries = new DocsQueries(db.getRawDb(), cwd);
+    const result = queries.getSection(id, { context: opts.context });
+    if (!result) {
+      const rawDb = db.getRawDb();
+      const idParts = id.split("::");
+      const filePath = idParts[0] ?? "";
+      const searchSlug = (idParts[1] ?? "").replace(/#\d+$/, "").split("/").pop() ?? "";
+      let suggestions = [];
+      if (searchSlug) {
+        suggestions = rawDb.all(
+          `SELECT id, title FROM doc_sections WHERE file_path = ? AND id LIKE ? LIMIT 5`,
+          [filePath, `%${searchSlug}%`]
+        );
+      }
+      if (suggestions.length === 0 && filePath) {
+        suggestions = rawDb.all(
+          `SELECT id, title FROM doc_sections WHERE file_path = ? ORDER BY position LIMIT 5`,
+          [filePath]
+        );
+      }
+      console.error(`  \u2716 Section "${id}" not found.`);
+      if (suggestions.length > 0) {
+        console.error(`
+  ${import_ui.dim}Did you mean:${import_ui.reset}`);
+        for (const s of suggestions) {
+          console.error(`    ${s.id}  ${import_ui.dim}(${s.title})${import_ui.reset}`);
+        }
+      } else {
+        console.error(`
+  ${import_ui.dim}Use ${import_ui.violet}kirograph docs toc${import_ui.reset}${import_ui.dim} to list available section IDs.${import_ui.reset}`);
+      }
+      safeCloseAndExit(cg, 1);
+    }
+    if (result.ancestors?.length) {
+      console.log(`  ${import_ui.dim}${result.ancestors.map((a) => a.title).join(" > ")} > ${result.section.title}${import_ui.reset}
+`);
+    }
+    console.log(result.content);
+    if (result.children?.length) {
+      console.log(`
+  ${import_ui.dim}Child sections:${import_ui.reset}`);
+      for (const child of result.children) {
+        const summary = child.summary ? ` \u2014 ${child.summary}` : "";
+        console.log(`    ${import_ui.dim}\u2022${import_ui.reset} ${child.title}${summary}`);
+      }
+    }
+    cg.close();
+  });
+  docs.command("outline <file>").description("Print heading hierarchy for a document").action(async (file) => {
+    const cwd = process.cwd();
+    const config = await (0, import_config.loadConfig)(cwd);
+    if (!config.enableDocs) {
+      console.error(`  \u2716 Documentation indexing is not enabled. Set ${import_ui.violet}${import_ui.bold}enableDocs: true${import_ui.reset} in .kirograph/config.json`);
+      process.exit(1);
+    }
+    const KiroGraph = (await Promise.resolve().then(() => require("../../index.js"))).default;
+    if (!KiroGraph.isInitialized(cwd)) {
+      console.error("  \u2716 KiroGraph not initialized.");
+      process.exit(1);
+    }
+    const cg = await KiroGraph.open(cwd);
+    const db = cg.getDatabase();
+    db.applyDocsSchema();
+    const { DocsQueries } = await Promise.resolve().then(() => require("../../docs/queries.js"));
+    const queries = new DocsQueries(db.getRawDb(), cwd);
+    const outline = queries.getOutline(file);
+    if (outline.length === 0) {
+      console.log(`  ${import_ui.dim}No sections found in "${file}".${import_ui.reset}`);
+      cg.close();
+      return;
+    }
+    console.log(`
+  ${import_ui.bold}${file}${import_ui.reset}
+`);
+    const render = (entries, indent) => {
+      for (const entry of entries) {
+        const summary = entry.summary ? ` ${import_ui.dim}\u2014 ${entry.summary}${import_ui.reset}` : "";
+        console.log(`${indent}  ${"#".repeat(entry.level || 1)} ${entry.title}${summary}`);
+        if (entry.children?.length) render(entry.children, indent + "  ");
+      }
+    };
+    render(outline, "");
+    cg.close();
+  });
+  docs.command("refs <id>").description("Show code \u2194 doc cross-references").action(async (id) => {
+    const cwd = process.cwd();
+    const config = await (0, import_config.loadConfig)(cwd);
+    if (!config.enableDocs) {
+      console.error(`  \u2716 Documentation indexing is not enabled. Set ${import_ui.violet}${import_ui.bold}enableDocs: true${import_ui.reset} in .kirograph/config.json`);
+      process.exit(1);
+    }
+    const KiroGraph = (await Promise.resolve().then(() => require("../../index.js"))).default;
+    if (!KiroGraph.isInitialized(cwd)) {
+      console.error("  \u2716 KiroGraph not initialized.");
+      process.exit(1);
+    }
+    const cg = await KiroGraph.open(cwd);
+    const db = cg.getDatabase();
+    db.applyDocsSchema();
+    const { DocsQueries } = await Promise.resolve().then(() => require("../../docs/queries.js"));
+    const queries = new DocsQueries(db.getRawDb(), cwd);
+    let refs = queries.getRefs({ sectionId: id });
+    if (refs.length === 0) {
+      refs = queries.getRefs({ qualifiedName: id });
+    }
+    if (refs.length === 0) {
+      console.log(`  ${import_ui.dim}No cross-references found for "${id}".${import_ui.reset}`);
+      cg.close();
+      return;
+    }
+    for (const r of refs) {
+      console.log(`  [${r.refType}] ${r.qualifiedName} ${import_ui.dim}(confidence: ${r.confidence.toFixed(2)})${import_ui.reset}`);
+    }
+    cg.close();
+  });
+  docs.command("reindex").description("Force re-index all documentation files").action(async () => {
+    const cwd = process.cwd();
+    const config = await (0, import_config.loadConfig)(cwd);
+    if (!config.enableDocs) {
+      console.error(`  \u2716 Documentation indexing is not enabled. Set ${import_ui.violet}${import_ui.bold}enableDocs: true${import_ui.reset} in .kirograph/config.json`);
+      process.exit(1);
+    }
+    const KiroGraph = (await Promise.resolve().then(() => require("../../index.js"))).default;
+    if (!KiroGraph.isInitialized(cwd)) {
+      console.error("  \u2716 KiroGraph not initialized.");
+      process.exit(1);
+    }
+    const cg = await KiroGraph.open(cwd);
+    const db = cg.getDatabase();
+    db.applyDocsSchema();
+    const { DocsIndexer } = await Promise.resolve().then(() => require("../../docs/indexer.js"));
+    const indexer = new DocsIndexer(db.getRawDb(), config, cwd);
+    console.log(`  ${import_ui.dim}Re-indexing documentation...${import_ui.reset}`);
+    const result = await indexer.indexAll({ force: true, onProgress: (msg) => console.log(`  ${import_ui.dim}${msg}${import_ui.reset}`) });
+    console.log(`  ${import_ui.green}\u2713${import_ui.reset} ${(0, import_ui.value)(String(result.filesIndexed))} ${import_ui.dim}files,${import_ui.reset} ${(0, import_ui.value)(String(result.sectionsCreated))} ${import_ui.dim}sections created,${import_ui.reset} ${(0, import_ui.value)(String(result.sectionsUpdated))} ${import_ui.dim}updated,${import_ui.reset} ${(0, import_ui.value)(String(result.sectionsRemoved))} ${import_ui.dim}removed${import_ui.reset} ${import_ui.dim}(${result.duration}ms)${import_ui.reset}`);
+    if (result.errors.length) {
+      console.warn(`  \x1B[33m\u26A0 ${result.errors.length} error(s)\x1B[0m`);
+      for (const err of result.errors.slice(0, 5)) console.warn(`    ${err}`);
+    }
+    cg.close();
+  });
+  docs.command("lint").description("Find broken refs, stale sections, FTS desync").action(async () => {
+    const cwd = process.cwd();
+    const config = await (0, import_config.loadConfig)(cwd);
+    if (!config.enableDocs) {
+      console.error(`  \u2716 Documentation indexing is not enabled. Set ${import_ui.violet}${import_ui.bold}enableDocs: true${import_ui.reset} in .kirograph/config.json`);
+      process.exit(1);
+    }
+    const KiroGraph = (await Promise.resolve().then(() => require("../../index.js"))).default;
+    if (!KiroGraph.isInitialized(cwd)) {
+      console.error("  \u2716 KiroGraph not initialized.");
+      process.exit(1);
+    }
+    const cg = await KiroGraph.open(cwd);
+    const db = cg.getDatabase();
+    db.applyDocsSchema();
+    const { docsLint } = await Promise.resolve().then(() => require("../../docs/lint.js"));
+    const result = docsLint(db.getRawDb(), cwd);
+    if (result.totalIssues === 0) {
+      console.log(`  ${import_ui.green}\u2713${import_ui.reset} No issues found.`);
+      cg.close();
+      return;
+    }
+    console.log(`  Found ${result.totalIssues} issue(s):
+`);
+    if (result.brokenRefs.length > 0) {
+      console.log(`  ${import_ui.bold}Broken code refs:${import_ui.reset} ${result.brokenRefs.length}`);
+      for (const ref of result.brokenRefs.slice(0, 10)) {
+        console.log(`    ${import_ui.dim}${ref.sectionId} \u2192 ${ref.qualifiedName}${import_ui.reset}`);
+      }
+      if (result.brokenRefs.length > 10) console.log(`    ${import_ui.dim}\u2026and ${result.brokenRefs.length - 10} more${import_ui.reset}`);
+    }
+    if (result.staleSections.length > 0) {
+      console.log(`  ${import_ui.bold}Stale sections:${import_ui.reset} ${result.staleSections.length}`);
+      for (const s of result.staleSections.slice(0, 10)) {
+        console.log(`    ${import_ui.dim}${s.filePath} \u2014 ${s.id}${import_ui.reset}`);
+      }
+      if (result.staleSections.length > 10) console.log(`    ${import_ui.dim}\u2026and ${result.staleSections.length - 10} more${import_ui.reset}`);
+    }
+    if (result.ftsDesync) {
+      console.log(`  ${import_ui.bold}FTS desync:${import_ui.reset} ${result.ftsDesync.sections} sections vs ${result.ftsDesync.ftsRows} FTS rows`);
+    }
+    if (result.orphanRefs > 0) {
+      console.log(`  ${import_ui.bold}Orphan refs:${import_ui.reset} ${result.orphanRefs}`);
+    }
+    console.log(`
+  ${import_ui.dim}Run ${import_ui.violet}${import_ui.bold}kirograph docs reindex${import_ui.reset}${import_ui.dim} to fix stale sections.${import_ui.reset}`);
+    cg.close();
+  });
+  docs.command("reembed").description("Re-embed all doc sections with the current model").action(async () => {
+    const cwd = process.cwd();
+    const config = await (0, import_config.loadConfig)(cwd);
+    if (!config.enableDocs) {
+      console.error(`  \u2716 Documentation indexing is not enabled. Set ${import_ui.violet}${import_ui.bold}enableDocs: true${import_ui.reset} in .kirograph/config.json`);
+      process.exit(1);
+    }
+    if (!config.enableEmbeddings) {
+      console.error(`  \u2716 Embeddings are not enabled. Set ${import_ui.violet}${import_ui.bold}enableEmbeddings: true${import_ui.reset} in .kirograph/config.json`);
+      process.exit(1);
+    }
+    const KiroGraph = (await Promise.resolve().then(() => require("../../index.js"))).default;
+    if (!KiroGraph.isInitialized(cwd)) {
+      console.error("  \u2716 KiroGraph not initialized.");
+      process.exit(1);
+    }
+    const cg = await KiroGraph.open(cwd);
+    const db = cg.getDatabase();
+    db.applyDocsSchema();
+    const rawDb = db.getRawDb();
+    const sections = rawDb.all("SELECT id, title, summary FROM doc_sections");
+    if (sections.length === 0) {
+      console.log(`  ${import_ui.dim}No doc sections to embed. Run ${import_ui.violet}${import_ui.bold}kirograph docs reindex${import_ui.reset}${import_ui.dim} first.${import_ui.reset}`);
+      cg.close();
+      return;
+    }
+    console.log(`  ${import_ui.dim}Re-embedding ${sections.length} doc sections...${import_ui.reset}`);
+    const { DocsVectorManager } = await Promise.resolve().then(() => require("../../docs/vectors.js"));
+    const vectorMgr = new DocsVectorManager(config, rawDb);
+    const embedded = await vectorMgr.reembed();
+    console.log(`  ${import_ui.green}\u2713${import_ui.reset} Embedded ${(0, import_ui.value)(String(embedded))} doc sections with model ${import_ui.dim}${config.embeddingModel}${import_ui.reset}`);
+    cg.close();
+  });
+}
+// Annotate the CommonJS export names for ESM import in node:
+0 && (module.exports = {
+  register
+});
+//# sourceMappingURL=docs.js.map

package/dist/bin/commands/docs.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../../src/bin/commands/docs.ts"],
+  "sourcesContent": ["import { Command } from 'commander';\nimport * as path from 'path';\nimport { loadConfig } from '../../config';\nimport { dim, reset, violet, bold, green, value } from '../ui';\n\n/** Safely close KiroGraph and exit cleanly. */\nfunction safeCloseAndExit(cg: any, code = 0): never {\n  try { cg.close(); } catch { /* ignore */ }\n  // Suppress any post-exit WASM crash output and exit cleanly\n  try {\n    const fs = require('fs');\n    // Flush stdout/stderr, then close fd 2 to suppress libc++abi messages\n    if (process.stdout.writableEnded === false) process.stdout.write('');\n    if (process.stderr.writableEnded === false) process.stderr.write('');\n    fs.closeSync(2);\n    fs.closeSync(1);\n  } catch { /* ignore */ }\n  process.exit(code);\n}\n\nexport function register(program: Command): void {\n  const docs = program\n    .command('docs')\n    .description('Documentation navigation (requires enableDocs: true)');\n\n  // \u2500\u2500 toc \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  docs\n    .command('toc [file]')\n    .description('Print table of contents for a file or the whole project')\n    .option('--tree', 'Show nested tree structure')\n    .option('--json', 'Output as JSON')\n    .action(async (file: string | undefined, opts: { tree?: boolean; json?: boolean }) => {\n      const cwd = process.cwd();\n      const config = await loadConfig(cwd);\n      if (!config.enableDocs) {\n        console.error(`  \u2716 Documentation indexing is not enabled. Set ${violet}${bold}enableDocs: true${reset} in .kirograph/config.json`);\n        console.error(`  ${dim}Then re-run:${reset} ${violet}${bold}kirograph index${reset}`);\n        process.exit(1);\n      }\n\n      const KiroGraph = (await Promise.resolve().then(() => require('../../index.js'))).default;\n      if (!KiroGraph.isInitialized(cwd)) { console.error('  \u2716 KiroGraph not initialized. Run: kirograph init'); process.exit(1); }\n      const cg = await KiroGraph.open(cwd);\n      const db = cg.getDatabase();\n      db.applyDocsSchema();\n\n      const { DocsQueries } = await Promise.resolve().then(() => require('../../docs/queries.js'));\n      const queries = new DocsQueries(db.getRawDb(), cwd);\n      const toc = queries.getToc({ file, tree: opts.tree });\n\n      if (toc.length === 0) {\n        console.log(`  ${dim}No documentation sections found.${reset} Run ${violet}${bold}kirograph index${reset} first.`);\n        cg.close(); return;\n      }\n\n      if (opts.json) {\n        console.log(JSON.stringify(toc, null, 2));\n      } else {\n        for (const entry of toc) {\n          const prefix = '#'.repeat(entry.level || 1);\n          const summary = entry.summary ? ` ${dim}\u2014 ${entry.summary}${reset}` : '';\n          console.log(`  ${prefix} ${bold}${entry.title}${reset}${summary}`);\n          console.log(`    ${dim}${entry.id}${reset}`);\n        }\n      }\n      cg.close();\n    });\n\n  // \u2500\u2500 search \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  docs\n    .command('search <query>')\n    .description('Search documentation sections')\n    .option('--file <path>', 'Narrow search to a specific file')\n    .option('--limit <n>', 'Max results', '10')\n    .option('--json', 'Output as JSON')\n    .action(async (query: string, opts: { file?: string; limit?: string; json?: boolean }) => {\n      const cwd = process.cwd();\n      const config = await loadConfig(cwd);\n      if (!config.enableDocs) {\n        console.error(`  \u2716 Documentation indexing is not enabled. Set ${violet}${bold}enableDocs: true${reset} in .kirograph/config.json`);\n        process.exit(1);\n      }\n\n      const KiroGraph = (await Promise.resolve().then(() => require('../../index.js'))).default;\n      if (!KiroGraph.isInitialized(cwd)) { console.error('  \u2716 KiroGraph not initialized.'); process.exit(1); }\n      const cg = await KiroGraph.open(cwd);\n      const db = cg.getDatabase();\n      db.applyDocsSchema();\n\n      const { DocsQueries } = await Promise.resolve().then(() => require('../../docs/queries.js'));\n      const queries = new DocsQueries(db.getRawDb(), cwd, config);\n      const results = await queries.searchSections(query, { file: opts.file, limit: parseInt(opts.limit ?? '10', 10) });\n\n      if (results.length === 0) {\n        console.log(`  ${dim}No sections found matching \"${query}\".${reset}`);\n        cg.close(); return;\n      }\n\n      if (opts.json) {\n        console.log(JSON.stringify(results, null, 2));\n      } else {\n        for (const r of results) {\n          const summary = r.section.summary ? `\\n    ${dim}${r.section.summary}${reset}` : '';\n          console.log(`  ${green}\u25CF${reset} ${bold}${r.section.title}${reset} ${dim}[${r.section.filePath}]${reset}${summary}`);\n          console.log(`    ${dim}ID: ${r.section.id}${reset}`);\n        }\n      }\n      cg.close();\n    });\n\n  // \u2500\u2500 section \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  docs\n    .command('section <id>')\n    .description('Print full content of a section by ID')\n    .option('--context', 'Include ancestor headings and child summaries')\n    .action(async (id: string, opts: { context?: boolean }) => {\n      const cwd = process.cwd();\n      const config = await loadConfig(cwd);\n      if (!config.enableDocs) {\n        console.error(`  \u2716 Documentation indexing is not enabled. Set ${violet}${bold}enableDocs: true${reset} in .kirograph/config.json`);\n        process.exit(1);\n      }\n\n      const KiroGraph = (await Promise.resolve().then(() => require('../../index.js'))).default;\n      if (!KiroGraph.isInitialized(cwd)) { console.error('  \u2716 KiroGraph not initialized.'); process.exit(1); }\n      const cg = await KiroGraph.open(cwd);\n      const db = cg.getDatabase();\n      db.applyDocsSchema();\n\n      const { DocsQueries } = await Promise.resolve().then(() => require('../../docs/queries.js'));\n      const queries = new DocsQueries(db.getRawDb(), cwd);\n      const result = queries.getSection(id, { context: opts.context });\n\n      if (!result) {\n        // Suggest similar section IDs\n        const rawDb = db.getRawDb();\n        const idParts = id.split('::');\n        const filePath = idParts[0] ?? '';\n        const searchSlug = (idParts[1] ?? '').replace(/#\\d+$/, '').split('/').pop() ?? '';\n\n        let suggestions: Array<{ id: string; title: string }> = [];\n        if (searchSlug) {\n          suggestions = rawDb.all(\n            `SELECT id, title FROM doc_sections WHERE file_path = ? AND id LIKE ? LIMIT 5`,\n            [filePath, `%${searchSlug}%`],\n          ) as Array<{ id: string; title: string }>;\n        }\n        if (suggestions.length === 0 && filePath) {\n          suggestions = rawDb.all(\n            `SELECT id, title FROM doc_sections WHERE file_path = ? ORDER BY position LIMIT 5`,\n            [filePath],\n          ) as Array<{ id: string; title: string }>;\n        }\n\n        console.error(`  \u2716 Section \"${id}\" not found.`);\n        if (suggestions.length > 0) {\n          console.error(`\\n  ${dim}Did you mean:${reset}`);\n          for (const s of suggestions) {\n            console.error(`    ${s.id}  ${dim}(${s.title})${reset}`);\n          }\n        } else {\n          console.error(`\\n  ${dim}Use ${violet}kirograph docs toc${reset}${dim} to list available section IDs.${reset}`);\n        }\n        safeCloseAndExit(cg, 1);\n      }\n\n      if (result.ancestors?.length) {\n        console.log(`  ${dim}${result.ancestors.map(a => a.title).join(' > ')} > ${result.section.title}${reset}\\n`);\n      }\n\n      console.log(result.content);\n\n      if (result.children?.length) {\n        console.log(`\\n  ${dim}Child sections:${reset}`);\n        for (const child of result.children) {\n          const summary = child.summary ? ` \u2014 ${child.summary}` : '';\n          console.log(`    ${dim}\u2022${reset} ${child.title}${summary}`);\n        }\n      }\n      cg.close();\n    });\n\n  // \u2500\u2500 outline \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  docs\n    .command('outline <file>')\n    .description('Print heading hierarchy for a document')\n    .action(async (file: string) => {\n      const cwd = process.cwd();\n      const config = await loadConfig(cwd);\n      if (!config.enableDocs) {\n        console.error(`  \u2716 Documentation indexing is not enabled. Set ${violet}${bold}enableDocs: true${reset} in .kirograph/config.json`);\n        process.exit(1);\n      }\n\n      const KiroGraph = (await Promise.resolve().then(() => require('../../index.js'))).default;\n      if (!KiroGraph.isInitialized(cwd)) { console.error('  \u2716 KiroGraph not initialized.'); process.exit(1); }\n      const cg = await KiroGraph.open(cwd);\n      const db = cg.getDatabase();\n      db.applyDocsSchema();\n\n      const { DocsQueries } = await Promise.resolve().then(() => require('../../docs/queries.js'));\n      const queries = new DocsQueries(db.getRawDb(), cwd);\n      const outline = queries.getOutline(file);\n\n      if (outline.length === 0) {\n        console.log(`  ${dim}No sections found in \"${file}\".${reset}`);\n        cg.close(); return;\n      }\n\n      console.log(`\\n  ${bold}${file}${reset}\\n`);\n      const render = (entries: any[], indent: string) => {\n        for (const entry of entries) {\n          const summary = entry.summary ? ` ${dim}\u2014 ${entry.summary}${reset}` : '';\n          console.log(`${indent}  ${'#'.repeat(entry.level || 1)} ${entry.title}${summary}`);\n          if (entry.children?.length) render(entry.children, indent + '  ');\n        }\n      };\n      render(outline, '');\n      cg.close();\n    });\n\n  // \u2500\u2500 refs \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  docs\n    .command('refs <id>')\n    .description('Show code \u2194 doc cross-references')\n    .action(async (id: string) => {\n      const cwd = process.cwd();\n      const config = await loadConfig(cwd);\n      if (!config.enableDocs) {\n        console.error(`  \u2716 Documentation indexing is not enabled. Set ${violet}${bold}enableDocs: true${reset} in .kirograph/config.json`);\n        process.exit(1);\n      }\n\n      const KiroGraph = (await Promise.resolve().then(() => require('../../index.js'))).default;\n      if (!KiroGraph.isInitialized(cwd)) { console.error('  \u2716 KiroGraph not initialized.'); process.exit(1); }\n      const cg = await KiroGraph.open(cwd);\n      const db = cg.getDatabase();\n      db.applyDocsSchema();\n\n      const { DocsQueries } = await Promise.resolve().then(() => require('../../docs/queries.js'));\n      const queries = new DocsQueries(db.getRawDb(), cwd);\n\n      // Try as section ID first, then as qualified name\n      let refs = queries.getRefs({ sectionId: id });\n      if (refs.length === 0) {\n        refs = queries.getRefs({ qualifiedName: id });\n      }\n\n      if (refs.length === 0) {\n        console.log(`  ${dim}No cross-references found for \"${id}\".${reset}`);\n        cg.close(); return;\n      }\n\n      for (const r of refs) {\n        console.log(`  [${r.refType}] ${r.qualifiedName} ${dim}(confidence: ${r.confidence.toFixed(2)})${reset}`);\n      }\n      cg.close();\n    });\n\n  // \u2500\u2500 reindex \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  docs\n    .command('reindex')\n    .description('Force re-index all documentation files')\n    .action(async () => {\n      const cwd = process.cwd();\n      const config = await loadConfig(cwd);\n      if (!config.enableDocs) {\n        console.error(`  \u2716 Documentation indexing is not enabled. Set ${violet}${bold}enableDocs: true${reset} in .kirograph/config.json`);\n        process.exit(1);\n      }\n\n      const KiroGraph = (await Promise.resolve().then(() => require('../../index.js'))).default;\n      if (!KiroGraph.isInitialized(cwd)) { console.error('  \u2716 KiroGraph not initialized.'); process.exit(1); }\n      const cg = await KiroGraph.open(cwd);\n      const db = cg.getDatabase();\n      db.applyDocsSchema();\n\n      const { DocsIndexer } = await Promise.resolve().then(() => require('../../docs/indexer.js'));\n      const indexer = new DocsIndexer(db.getRawDb(), config, cwd);\n\n      console.log(`  ${dim}Re-indexing documentation...${reset}`);\n      const result = await indexer.indexAll({ force: true, onProgress: msg => console.log(`  ${dim}${msg}${reset}`) });\n\n      console.log(`  ${green}\u2713${reset} ${value(String(result.filesIndexed))} ${dim}files,${reset} ${value(String(result.sectionsCreated))} ${dim}sections created,${reset} ${value(String(result.sectionsUpdated))} ${dim}updated,${reset} ${value(String(result.sectionsRemoved))} ${dim}removed${reset} ${dim}(${result.duration}ms)${reset}`);\n      if (result.errors.length) {\n        console.warn(`  \\x1b[33m\u26A0 ${result.errors.length} error(s)\\x1b[0m`);\n        for (const err of result.errors.slice(0, 5)) console.warn(`    ${err}`);\n      }\n      cg.close();\n    });\n\n  // \u2500\u2500 lint \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  docs\n    .command('lint')\n    .description('Find broken refs, stale sections, FTS desync')\n    .action(async () => {\n      const cwd = process.cwd();\n      const config = await loadConfig(cwd);\n      if (!config.enableDocs) {\n        console.error(`  \u2716 Documentation indexing is not enabled. Set ${violet}${bold}enableDocs: true${reset} in .kirograph/config.json`);\n        process.exit(1);\n      }\n\n      const KiroGraph = (await Promise.resolve().then(() => require('../../index.js'))).default;\n      if (!KiroGraph.isInitialized(cwd)) { console.error('  \u2716 KiroGraph not initialized.'); process.exit(1); }\n      const cg = await KiroGraph.open(cwd);\n      const db = cg.getDatabase();\n      db.applyDocsSchema();\n\n      const { docsLint } = await Promise.resolve().then(() => require('../../docs/lint.js'));\n      const result = docsLint(db.getRawDb(), cwd);\n\n      if (result.totalIssues === 0) {\n        console.log(`  ${green}\u2713${reset} No issues found.`);\n        cg.close(); return;\n      }\n\n      console.log(`  Found ${result.totalIssues} issue(s):\\n`);\n\n      if (result.brokenRefs.length > 0) {\n        console.log(`  ${bold}Broken code refs:${reset} ${result.brokenRefs.length}`);\n        for (const ref of result.brokenRefs.slice(0, 10)) {\n          console.log(`    ${dim}${ref.sectionId} \u2192 ${ref.qualifiedName}${reset}`);\n        }\n        if (result.brokenRefs.length > 10) console.log(`    ${dim}\u2026and ${result.brokenRefs.length - 10} more${reset}`);\n      }\n\n      if (result.staleSections.length > 0) {\n        console.log(`  ${bold}Stale sections:${reset} ${result.staleSections.length}`);\n        for (const s of result.staleSections.slice(0, 10)) {\n          console.log(`    ${dim}${s.filePath} \u2014 ${s.id}${reset}`);\n        }\n        if (result.staleSections.length > 10) console.log(`    ${dim}\u2026and ${result.staleSections.length - 10} more${reset}`);\n      }\n\n      if (result.ftsDesync) {\n        console.log(`  ${bold}FTS desync:${reset} ${result.ftsDesync.sections} sections vs ${result.ftsDesync.ftsRows} FTS rows`);\n      }\n\n      if (result.orphanRefs > 0) {\n        console.log(`  ${bold}Orphan refs:${reset} ${result.orphanRefs}`);\n      }\n\n      console.log(`\\n  ${dim}Run ${violet}${bold}kirograph docs reindex${reset}${dim} to fix stale sections.${reset}`);\n      cg.close();\n    });\n\n  // \u2500\u2500 reembed \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  docs\n    .command('reembed')\n    .description('Re-embed all doc sections with the current model')\n    .action(async () => {\n      const cwd = process.cwd();\n      const config = await loadConfig(cwd);\n      if (!config.enableDocs) {\n        console.error(`  \u2716 Documentation indexing is not enabled. Set ${violet}${bold}enableDocs: true${reset} in .kirograph/config.json`);\n        process.exit(1);\n      }\n      if (!config.enableEmbeddings) {\n        console.error(`  \u2716 Embeddings are not enabled. Set ${violet}${bold}enableEmbeddings: true${reset} in .kirograph/config.json`);\n        process.exit(1);\n      }\n\n      const KiroGraph = (await Promise.resolve().then(() => require('../../index.js'))).default;\n      if (!KiroGraph.isInitialized(cwd)) { console.error('  \u2716 KiroGraph not initialized.'); process.exit(1); }\n      const cg = await KiroGraph.open(cwd);\n      const db = cg.getDatabase();\n      db.applyDocsSchema();\n\n      const rawDb = db.getRawDb();\n      const sections = rawDb.all('SELECT id, title, summary FROM doc_sections') as Array<{ id: string; title: string; summary: string | null }>;\n\n      if (sections.length === 0) {\n        console.log(`  ${dim}No doc sections to embed. Run ${violet}${bold}kirograph docs reindex${reset}${dim} first.${reset}`);\n        cg.close(); return;\n      }\n\n      console.log(`  ${dim}Re-embedding ${sections.length} doc sections...${reset}`);\n      const { DocsVectorManager } = await Promise.resolve().then(() => require('../../docs/vectors.js'));\n      const vectorMgr = new DocsVectorManager(config, rawDb);\n      const embedded = await vectorMgr.reembed();\n      console.log(`  ${green}\u2713${reset} Embedded ${value(String(embedded))} doc sections with model ${dim}${config.embeddingModel}${reset}`);\n      cg.close();\n    });\n}\n"],
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+  "names": []
+}

package/dist/bin/installer/config-prompt.js

@@ -63,7 +63,7 @@ async function promptConfigOptions(rl) {
     "Semantic embeddings (similarity search):",
     "Enables natural-language code search via vector embeddings. A local model (~130MB) is downloaded on first use."
   );
-  const patch = { enableEmbeddings, useVecIndex: false, semanticEngine: "cosine", typesenseDashboard: false, qdrantDashboard: false, extractDocstrings: true, trackCallSites: true, enableArchitecture: false, cavemanMode: "off", shellCompressionLevel: "normal", enableMemory: false };
+  const patch = { enableEmbeddings, useVecIndex: false, semanticEngine: "cosine", typesenseDashboard: false, qdrantDashboard: false, extractDocstrings: true, trackCallSites: true, enableArchitecture: false, cavemanMode: "off", shellCompressionLevel: "normal", enableMemory: false, enableDocs: false, docsContextLimit: 0 };
   if (enableEmbeddings) {
     const modelChoice = await (0, import_prompts.arrowSelect)(
       rl,
@@ -146,6 +146,22 @@ async function promptConfigOptions(rl) {
     "Detects packages from manifests and architectural layers. Enables kirograph_architecture, kirograph_coupling, kirograph_package.",
     false
   );
+  (0, import_prompts.printSection)("\u{1F4D6}", "Documentation");
+  patch.enableDocs = await (0, import_prompts.askToggle)(
+    rl,
+    "Documentation indexing (section-level retrieval):",
+    "Indexes docs by heading structure. Enables kirograph_docs_toc, kirograph_docs_search, kirograph_docs_section, kirograph_docs_outline, kirograph_docs_refs.",
+    false
+  );
+  if (patch.enableDocs) {
+    const contextChoice = await (0, import_prompts.arrowSelect)(rl, "Include doc sections in kirograph_context results?", [
+      { value: 0, label: "0 (disabled)", description: "Docs stay separate \u2014 use kirograph_docs_* tools explicitly (recommended)" },
+      { value: 3, label: "3 sections", description: "Include up to 3 relevant doc sections in context results" },
+      { value: 5, label: "5 sections", description: "Include up to 5 relevant doc sections in context results" },
+      { value: 10, label: "10 sections", description: "Include up to 10 relevant doc sections in context results" }
+    ]);
+    patch.docsContextLimit = contextChoice;
+  }
   (0, import_prompts.printSection)("\u{1F916}", "Agent Behavior");
   const cavemanChoice = await (0, import_prompts.arrowSelect)(rl, "Communication style (caveman mode):", [
     { value: "off", label: "off", description: "Normal responses \u2014 no compression" },