chore: final root hygiene and drop openspec from VCS

Remove root build_mcp wrappers, stop tracking openspec and the
duplicate projects/python_kb tree, slim repo-root config/ to keys+README,
and move the LSP troubleshooting note under docs/. Update CI, packaging,
and docs to match the cleaned layout.

Author: bx33661

.github/workflows/ci.yml

@@ -38,10 +38,8 @@ jobs:
         run: uv run pytest -q
 
       - name: Compile Python modules
-        run: uv run python -m compileall -q Analyze.py api core services utils pure_auto_codeql tools
+        run: uv run python -m compileall -q Analyze.py pure_auto_codeql
 
-      - name: Validate OpenSpec
-        run: uv run openspec validate --all --strict
 
       - name: Check diff whitespace
         run: git diff --check

.gitignore

@@ -55,17 +55,17 @@ tmp/
 output/
 results/
 
-# 案例工作区：默认忽略，仅跟踪模板与内置 KB
+# 案例工作区：默认忽略，仅跟踪模板
 projects/*
 !projects/README.md
 !projects/case-template/
 !projects/case-template/**
-!projects/python_kb/
-!projects/python_kb/**
 
 # OS
 .DS_Store
 Thumbs.db
 .projects/
 *.zip
-utils/lsp
+
+# OpenSpec local workspace (not versioned)
+openspec/

AGENTS.md

@@ -1,18 +1,11 @@
-<!-- OPENSPEC:START -->
-# OpenSpec Instructions
+# Agent notes
 
-These instructions are for AI assistants working in this project.
+Runtime application code lives under `pure_auto_codeql/`.
 
-Always open `@/openspec/AGENTS.md` when the request:
-- Mentions planning or proposals (words like proposal, spec, change, plan)
-- Introduces new capabilities, breaking changes, architecture shifts, or big performance/security work
-- Sounds ambiguous and you need the authoritative spec before coding
+- Prefer: `from pure_auto_codeql.configuration import get_llm_config, LLMRole`
+- Prefer: `from pure_auto_codeql.utils...`, `pure_auto_codeql.services...`, etc.
+- User secrets: repo-root `config/keys.toml` (template: `config/keys.example.toml`)
+- CLI: `uv run pure-auto-codeql ...` or `python Analyze.py ...`
+- API: `uvicorn pure_auto_codeql.api.server:app`
 
-Use `@/openspec/AGENTS.md` to learn:
-- How to create and apply change proposals
-- Spec format and conventions
-- Project structure and guidelines
-
-Keep this managed block so 'openspec update' can refresh the instructions.
-
-<!-- OPENSPEC:END -->
+See `docs/package_architecture.md` for the package layout.

README.md

@@ -265,10 +265,10 @@ PureAutoCodeQL/
 │   ├── information/ prompts/ services/ tools/ utils/
 │   ├── configuration.py paths.py
 │   └── …
-├── config/                    # keys.toml / keys.example.toml / 配置说明
-├── tools/mcp_ripgrep/         # Node MCP 工具（构建脚本仍指向此处）
+├── config/                    # keys.example.toml + 本地 keys.toml（不入库）
+├── tools/mcp_ripgrep/         # Node MCP 工具
 ├── docs/ resources/ scripts/ docker/
-├── projects/ examples/ openspec/ test/
+├── projects/case-template/ examples/ test/
 └── README / pyproject.toml / …
 ```
 
@@ -285,14 +285,15 @@ PureAutoCodeQL/
 | [docs/path_selection_run_guide.md](docs/path_selection_run_guide.md) | 路径精选模块运行说明 |
 | [docs/extra_input_files_simple.md](docs/extra_input_files_simple.md) | `inputs/` 额外上下文文件 |
 | [docs/cpp/CPP_TWO_STEP_BUILD_GUIDE.md](docs/cpp/CPP_TWO_STEP_BUILD_GUIDE.md) | C/C++ 两步走建库策略 |
+| [docs/codeql_lsp_troubleshooting.md](docs/codeql_lsp_troubleshooting.md) | CodeQL LSP 启动问题排查 |
 | [docs/archive/](docs/archive/) | 历史设计方案、诊断笔记和阶段性总结 |
 
 ## 测试
 
 ```bash
 uv run pytest -q
 uv lock --check
-uv run python -m compileall -q Analyze.py pure_auto_codeql config
+uv run python -m compileall -q Analyze.py pure_auto_codeql
 ```
 
 ## 配置导入约定

build_mcp.bat

@@ -1,14 +1,11 @@
 """Legacy script shim for the configuration CLI.
 
 Runtime application code should import configuration helpers from
-`pure_auto_codeql.configuration`. The `config/` package remains available for
-legacy `from config import ...` imports, and this root-level file is kept so
-`python config.py ...` continues to launch the configuration CLI.
+`pure_auto_codeql.configuration`. User keys live in repo-root `config/keys.toml`.
+This file only keeps `python config.py ...` working.
 """
 
-from config import *  # noqa: F401, F403
-
 if __name__ == "__main__":
-    from config.cli import main
+    from pure_auto_codeql.config.cli import main
 
     main()