Tune madoqua

Reference for what madoqua runs and what it reports. Everything here is repo-wide policy unless it is in the personal overlay.

Layers. Built-in defaults, [tool.madoqua] in pyproject.toml, the uncommitted overlay hooks.local.toml in the git directory (<repo>/.git, or the clone’s in a linked worktree), then MADOQUA_SKIP. Later layers win.

fix and check replace that phase’s list entirely; extend_fix and extend_check append to it, after the replacement. Scalar keys such as log: the later layer wins. A layer silent about a key leaves it alone.

The registry. An entry is a command line, or a table with these keys:

Key	Default	Meaning
`cmd`	-	The command line. Required in table form.
`name`	leading non-flag words of `cmd`	What the verdict, the log and `MADOQUA_SKIP` call this step.
`on`	`[".py", ".pyi"]`	Globs for the staged files that wake this step. Replaces the default.
`pass_files`	true	Append the files `on` matched. Set it false for tools that scope themselves.
`timeout_s`	none	Kill the step after this many seconds. Killed is failed.
`max_output_lines`	none	Keep this many lines of a failure and truncate the rest. This is the knob for fitting a failure into an agent’s context window.
`when`	`always`	Checks only. `commit`: only in the hook; `full`: only in `madoqua check`.
`full_cmd`	`cmd`	Checks only. What `madoqua check` runs instead, with no file list.
`blocking`	true	Checks only. false: never fails the run; its output is shown even on a pass.

on and the file list. A step runs only if a staged file matches its on, and gets those files after its arguments: ruff check --quiet a.py. Globs as in .gitignore: no / matches the name at any depth, * stays in one directory, ** spans many. With no match anywhere there is no run at all - no output, no log row, exit 0. No shell: |, ; and && are refused.

The whole repo. madoqua check runs every check as if every file were staged (tracked, or untracked and not ignored), and fixes, stages and logs nothing. The siblings, set up for both runs:

[tool.madoqua]
extend_check = [
  { name = "biston", cmd = "biston scan --focus-args", full_cmd = "biston scan ." },
  { name = "zorilla", cmd = "zorilla check" },
  { name = "gerenuk", cmd = "gerenuk run -- -q", pass_files = false, when = "commit",
    on = ["*.py", "uv.lock", "pyproject.toml"], timeout_s = 120 },
  { name = "pytest", cmd = "pytest -q", pass_files = false, when = "full" },
  { name = "pysentry", cmd = "pysentry-rs .", pass_files = false, when = "full",
    blocking = false },
]

Phases. Fixers run in order, only their files are re-staged, and only a fixer that could not start blocks. Checks run in parallel; non-zero blocks.

Skipping. MADOQUA_SKIP="ty check" drops checks by exact name for one run, and never touches the fix phase. log defaults to hook-timings.jsonl in the git directory; point it under ~ to pool every repo’s runs, which madoqua stats --repo=<name> filters. Rows are sorted by p95 descending.

next: run madoqua stats

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