fix(mcp-server): route diagnostics to stderr to fix stdio protocol crash

[annopick]

中文

本 PR 修复 mcp-server 的两个启动即崩溃问题，并补齐打包缺陷。修复版本已发布到 PyPI：weknora-mcp 1.0.1。

修复 1：stdio 协议流被诊断输出破坏

入口脚本（run_server.py、main.py、run.py）通过裸 print() 把诊断信息写到了 stdout。在 stdio 传输下（默认传输，也是 MCP_CONFIG.md 中所有 MCP 客户端的启动方式 uv run run_server.py），stdout 是 JSON-RPC 通道，客户端期望 stdout 每一行都是合法的 JSON-RPC。握手前打到 stdout 的纯文本行破坏了协议流，严格客户端（Claude Desktop / Cursor / ZCode / VS Code Copilot）据此判定协议错误 → "服务器启动失败" → 启动即崩溃。

原始字节证据（PYTHONUNBUFFERED=1 + hex dump）：

修复前 stdout 开头: e5 90 af e5 8a a8 20 ... → "启动 WeKnora MCP Server..."（纯文本）
修复后 stdout 开头: 7b 22 6a 73 6f 6e ...    → {"jsonrpc":"2.0"...（合法 JSON-RPC）

按 MCP 规范，所有诊断 print() 改到 sys.stderr，stdout 仅保留 JSON-RPC。weknora_mcp_server.py 用的是 logging（已走 stderr），未改动。

修复 2：wheel 漏打包 upload_paths.py

[tool.setuptools] py-modules 和 setup.py 的 py_modules 列表都漏了 upload_paths，setuptools 不会打包它。而 weknora_mcp_server.py:26 有 from upload_paths import ...，所以任何走完整导入的启动（即 MCP 客户端 initialize 握手）都会 ModuleNotFoundError 崩溃。--version 不崩是因为 argparse 在导入前就 exit 了。已发布的 1.0.0 wheel 实测确认 upload_paths.py 缺失。

修复：两处 py-modules/py_modules 都补上 upload_paths。已排查所有顶层 .py，确认只有 upload_paths 是真正缺失的运行时模块（__init__.py 是包标记、setup.py 是构建脚本，按设计都不打包）。

版本

包名 weknora-mcp，版本 1.0.0 → 1.0.1（PyPI 不允许覆盖已发布版本）。同步 __version__、server_version、--version 三处用户可见版本串。console-script 命令（weknora-mcp-server、weknora-server）与 Python 模块名 weknora_mcp_server 保持不变，向后兼容。

验证

1. stdout 纯净性：hex dump 首字节为 7b({)，诊断文本全部落到 stderr
2. 完整握手（针对真实后端）：initialize → tools/list(28 tools) → tools/call list_knowledge_bases(success, 4 个知识库) 全链路成功
3. 打包修复：1.0.1 wheel 实测含 upload_paths.py（1.0.0 缺失）；干净 venv 安装后 from upload_paths import ... 解析成功
4. 回归：main.py stdio 同样纯净；--check-only 输出仍在终端可见（stderr）

改动范围

仅 mcp-server/ 下 6 个文件，无后端逻辑变更。

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English

This PR fixes two crash-on-startup issues in mcp-server and a packaging defect. The fixed release is published on PyPI: weknora-mcp 1.0.1.

Fix 1: stdio protocol stream corrupted by diagnostics

Entry scripts (run_server.py, main.py, run.py) wrote diagnostics to stdout via bare print(). Under the stdio transport (the default, and the path used by all MCP clients per MCP_CONFIG.md: uv run run_server.py), stdout is the JSON-RPC channel — clients expect every stdout line to be valid JSON-RPC. Plain-text lines emitted before the initialize handshake corrupted the stream, so strict clients (Claude Desktop / Cursor / ZCode / VS Code Copilot) treated it as a fatal protocol error → "server failed to start" → crash on startup.

Raw-byte evidence (PYTHONUNBUFFERED=1 + hex dump):

before: stdout starts with e5 90 af e5 8a a8 20 ... → "启动 WeKnora MCP Server..." (plain text)
after:  stdout starts with 7b 22 6a 73 6f 6e ...    → {"jsonrpc":"2.0"... (valid JSON-RPC)

Per the MCP spec, all diagnostic print() now goes to sys.stderr; stdout is reserved for JSON-RPC. weknora_mcp_server.py already routes through logging (stderr) and is unchanged.

Fix 2: wheel missing upload_paths.py

Both the [tool.setuptools] py-modules list and setup.py's py_modules omitted upload_paths, so setuptools never packed it. But weknora_mcp_server.py:26 does from upload_paths import ..., so any path that fully imports the module — i.e. the MCP client initialize handshake — crashed with ModuleNotFoundError. --version survived only because argparse exits before that import runs. The published 1.0.0 wheel was confirmed to be missing upload_paths.py.

Fix: add upload_paths to both py-modules/py_modules. All top-level .py files were audited; only upload_paths was a genuinely missing runtime module (__init__.py is a package marker, setup.py is the build script — neither is packed by design).

Versioning

Package weknora-mcp, version 1.0.0 → 1.0.1 (PyPI forbids overwriting published versions). The user-facing version strings (__version__, server_version, --version) are synced to 1.0.1. Console-script commands (weknora-mcp-server, weknora-server) and the Python module name weknora_mcp_server are unchanged for backward compatibility.

Verification

1. stdout purity: hex dump first byte is 7b ({); all diagnostics land on stderr
2. full handshake (against a live backend): initialize → tools/list (28 tools) → tools/call list_knowledge_bases (success, 4 KBs) all succeed
3. packaging fix: the 1.0.1 wheel contains upload_paths.py (1.0.0 did not); after a clean-venv install, from upload_paths import ... resolves
4. regression: main.py stdio is equally clean; --check-only output still visible on stderr

Scope

Only 6 files under mcp-server/; no backend logic changes.