fix: baseline lint coverage changes

[zeitlinger]

Summary

Fixes #213.

• run newly active linters against all matching files once so migrations establish a baseline
• run affected linters against all files when their config changes
• distinguish global flint.toml settings changes from per-check special config changes
• run ShellCheck with -x -P SCRIPTDIR so sourced sibling files resolve correctly
• add regression fixtures for new-linter, linter-config, global flint settings, and ShellCheck sourced-file cases
• sync Renovate's linter package grouping with the current registry

Validation

• FLINT_CASES=general/baseline-flint-settings-change cargo test cases
• FLINT_CASES=general/baseline-new-linter cargo test cases
• FLINT_CASES=general/baseline-config-change cargo test cases
• FLINT_CASES=shellcheck cargo test cases
• mise run test
• mise run lint:fix

[Copilot]

Pull request overview

Implements baseline lint coverage behavior so that newly-activated linters and linter/config changes trigger a one-time full-file run to establish a consistent baseline (including improving ShellCheck source resolution), and adds regression fixtures to lock in the behavior.

Changes:

• Add baseline selection logic so newly active linters and relevant config changes run against all matching files once.
• Update ShellCheck invocation to follow sourced files using -x -P SCRIPTDIR.
• Add/extend end-to-end regression fixtures for baseline scenarios and ShellCheck sourced-file behavior; update Renovate linter grouping.

Reviewed changes

Copilot reviewed 25 out of 25 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/cases/shellcheck/sourced-file/test.toml	Adds a ShellCheck fixture asserting sourced-file handling succeeds in --full mode.
tests/cases/shellcheck/sourced-file/files/mise.toml	Declares ShellCheck tool for the sourced-file fixture repo.
tests/cases/shellcheck/sourced-file/files/docker/run-pyroscope.sh	Provides a shell script that sources a sibling file to exercise ShellCheck -x resolution.
tests/cases/shellcheck/sourced-file/files/docker/logging.sh	Sourced shell file used by the sourced-file fixture.
tests/cases/general/baseline-new-linter/test.toml	Adds fixture asserting a newly enabled linter establishes baseline by scanning all relevant files.
tests/cases/general/baseline-new-linter/files/mise.toml	Baseline repo state without the newly enabled linter tool declared.
tests/cases/general/baseline-new-linter/files/bad.sh	Introduces a shell script that intentionally fails ShellCheck to validate baseline behavior.
tests/cases/general/baseline-new-linter/changes/mise.toml	Enables ShellCheck in the fixture’s “changed” state to simulate a newly activated linter.
tests/cases/general/baseline-flint-settings-change/test.toml	Adds fixture for baseline behavior triggered by global flint.toml settings changes.
tests/cases/general/baseline-flint-settings-change/files/mise.toml	Declares ShellCheck tool for the settings-change baseline fixture.
tests/cases/general/baseline-flint-settings-change/files/config/flint.toml	Fixture flint settings that exclude a failing file initially.
tests/cases/general/baseline-flint-settings-change/files/bad.sh	ShellCheck-failing file used to validate settings-change baseline behavior.
tests/cases/general/baseline-flint-settings-change/changes/config/flint.toml	Fixture change that updates global settings (exclude list) to trigger a baseline run.
tests/cases/general/baseline-config-change/test.toml	Adds fixture for baseline behavior triggered by linter-specific config changes.
tests/cases/general/baseline-config-change/files/mise.toml	Declares ShellCheck tool for the linter-config-change fixture.
tests/cases/general/baseline-config-change/files/config/.shellcheckrc	Fixture linter config initially disabling SC2086.
tests/cases/general/baseline-config-change/files/bad.sh	ShellCheck-failing file used to validate config-change baseline behavior.
tests/cases/general/baseline-config-change/changes/config/.shellcheckrc	Fixture change that re-enables SC2086 to trigger baseline behavior.
src/runner.rs	Makes RunOptions Copy/Clone to support reuse when partitioning baseline vs normal runs.
src/registry/mod.rs	Re-exports read_mise_tools_at_ref for baseline detection logic.
src/registry/mise.rs	Adds ability to read mise.toml tool declarations from a git ref (git show).
src/registry/checks.rs	Updates ShellCheck command template to shellcheck -x -P SCRIPTDIR {FILE}.
src/main.rs	Implements baseline selection logic and routes execution through a helper that runs baseline checks against an all-files list.
src/files.rs	Adds files::all() helper and uses it for the --full and “no merge base” fallback paths.
default.json	Updates Renovate linter package grouping to match the current tool keys/names.

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