Fix event loop warning filter and example configs

[jlowin]

Fixes the "Event loop is closed" warning that appears in CI when running MCP tests.

Changes

Warning suppression fix:

• Fixed malformed filterwarnings syntax - message regex was in wrong position

MCP provider improvements:

• Set keep_alive=False for stdio MCP servers to ensure proper subprocess cleanup on context exit
• Points to fastmcp main branch which includes keep_alive passthrough support

Better error reporting:

• Invalid frontmatter errors now show the filename (e.g., Invalid frontmatter in metrics_api.md:)

Examples fixes:

• Fixed examples/everything/colin.toml config format (model-path/output-path instead of [paths])
• Fixed all ref() calls to include .md extension
• Fixed output: json → output: {format: json} in metrics_api.md
• Created examples/mcp/ for isolated MCP testing

Root cause

The warning occurs because asyncio's BaseSubprocessTransport.__del__ runs after the event loop closes on Linux. The subprocess IS properly terminated, but the Python transport object's cleanup is deferred to GC. This is a timing issue in the asyncio/anyio/MCP SDK interaction that can't be fully fixed from colin's side - the filter is the pragmatic solution.

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Use project-relative MCP server path

The MCP command arg points to examples/mcp/mcp_server.py, but this config’s project root is examples/mcp and colin run uses the current directory as the project by default, so running the example from its own directory resolves the path to examples/mcp/examples/mcp/mcp_server.py and uvx cannot find the script. This only works when invoked from the repo root with an explicit project path; use a project-relative path like mcp_server.py (or set a cwd) so the example works when run from examples/mcp.

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