Introduce a project-local AI knowledge folder and fix Windows SQLite FTS5 issue.

- Add .ai/* docs (MEMORY, claude_rules, decisions, handover, repo_map, task_log, token_saving_rules) to record project memory, rules, ADRs and onboarding guidance.
- Update .gitignore to exclude .ai temporary/session files.
- Add better-sqlite3 as a supported backend (package.json updated) and implement runtime FTS5 detection + fallback in src/db/sqlite-adapter.ts (BetterSqlite3Adapter, nodeSqliteSupportsFts5, createDatabase changes).
- Fix backend display/logic in CLI and MCP tools (src/bin/codegraph.ts, src/mcp/tools.ts) to reflect dynamic backend selection.
- Minor build/install artifacts and scripts updated to support the changes (wasm asset, scripts, install.sh mode change).

Purpose: persist project-specific AI guidance to reduce repeated context rebuilding, and make CodeGraph usable on Windows Node 22.x where node:sqlite lacks FTS5 by falling back to better-sqlite3.

… FTS5

Node.js 22.x on Windows ships node:sqlite without ENABLE_FTS5, causing
codegraph init to fail with 'no such module: fts5'. Add runtime detection
and automatic fallback to better-sqlite3 when FTS5 is unavailable.

Also fix status commands (CLI + MCP) that hardcoded 'node-sqlite' backend
label instead of reporting the actual active backend.

Fix tests that assumed node-sqlite backend on all platforms, and add
missing cg.close()/db.close() calls that caused EBUSY on Windows.

- sqlite-backend.test.ts: dynamic backend detection
- node-sqlite-backend.test.ts: accept better-sqlite3 as valid backend
- frameworks-integration.test.ts: add missing cg.close() in JVM tests
- resolution.test.ts: close extra DB connection in C/C++ e2e test

Co-Authored-By: Claude Opus 4.8 <[email protected]>

创建通用永久能力模板，方便在其他项目中复用 CodeGraph 工作方式：

- docs/permanent-capability-template.md: 完整通用模板（开工九步、Token红线、
  各平台配置速查、任务模板）
- docs/setup-guide.md: 新项目部署指南（三种方案 + FAQ）
- .ai/codex_rules.md: CodeGraph 项目的 Codex 专用规则

重要修正：所有安装指令从官方 npm 包改为本地 fork 源码。
Windows 上官方 node:sqlite 缺少 FTS5，必须用本地 better-sqlite3 fallback。

- 前置条件：先 cd <workspace_root>/KnowledgeRoots/colbymchenry/codegraph
  执行 npm run build && npm link
- 去掉 raw.githubusercontent.com / codegraph.dev / npm install -g 等官方链接
- 新增 FAQ 解释为什么不能用官方包，以及换机器时路径处理

Co-Authored-By: Claude Opus 4.8 <[email protected]>

Document a startup guard for Codex projects: check codegraph status first, sync only when pending changes exist, and initialize only when a project has no index. This avoids rebuilding indexes on every session while still ensuring new projects get indexed.

Also record the GitHub CLI installation and global Codex MCP setup in the project handover and task log.

Update the project handover and task log after the Codex on-demand indexing docs were pushed successfully. Keep the remaining note that gh itself is installed but not authenticated for PR/API use.

Add the project-level AGENTS.md guidance plus local Codex skill definitions for adding languages and running agent evaluations. Include the agent-eval corpus so the skills can run from the repository context.

Record the GitHub CLI authentication check and the successful publish of AGENTS.md plus the local .agents skills in the project handover and task log.

Introduce a standard local query API for shared symbol search, file listing, status, callers, callees, and impact queries. Route the CLI and MCP tools through that API so MCP remains a compatibility adapter instead of owning separate business logic. Document the MCP transport fallback rule and add focused tests for the local API and Transport closed guidance.

Extend the local query API and CLI to support building task contexts and finding affected tests. Key changes:

- src/query/local-api.ts: add getFileDependents/buildContext to LocalQuerySource, introduce AffectedTestsResult, and implement findAffectedTests and buildTaskContext on CodeGraphLocalQueryApi.
- src/bin/codegraph.ts: add new `context` CLI command (buildTaskContext) and refactor `affected` to call api.findAffectedTests (removed inline BFS/test-detection logic).
- __tests__/local-query-api.test.ts: add tests for findAffectedTests and buildTaskContext.
- .ai/handover.md / .ai/task_log.md: update handover and task log with CC/Claude Code fallback guidance and notes about the local API/CLI/MCP adapter approach.

These changes centralize context/affected logic in the local API, simplify the CLI, and add documentation and tests to validate behavior.

Four modified skill entries passed the official skill validator; local instruction links were checked.

Validation: staged diff check passed. Commit only the reviewed repository content; retain local Goal overlays, reference links, backups and temporary outputs.