ponder-lab / Hybridize-Functions-Refactoring / #3239
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#3239

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Read each subject's trim from the manifest and apply it from the commit (#995)

* Read each subject's trim from the manifest and apply it from the commit

A subject's trim (`sparse`, `caller_scope_complete`, `exclude` and
`trim_note`) now comes from its manifest entry, so a committed manifest
is the whole description of what each run analyzes. `--config` keeps
only what is local to one machine, a `source` checkout, and refuses a
trim field.

`sparse` was only recorded before: the trim came from whichever sparse
clone `source` named. Its patterns are now applied by the harness,
reading the matching files from the commit itself, so how the local
checkout happens to be sparse no longer matters.

`--subjects-dir` and `--ground-truth` say where the checkouts and the
evaluated specs live, defaulting to the manifest's directory as before.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01NTnpjPjJj2aZy1ZkUD1eAn

* Let git apply a sparse trim, and refuse a malformed one

A hand-written matcher could not follow git's non-cone semantics: a
pattern matching a directory selects everything under it, so `/pkg/**`
or `/a/b` silently selected fewer files than git would. `git archive`
also applied export attributes, dropping an `export-ignore` file, and
passed every path on the command line.

A throwaway clone that shares the checkout's objects now takes the
patterns through `git sparse-checkout set --no-cone` and checks out HEAD,
so a pattern means exactly what it means to git. Nothing is written to
the checkout, lazy fetching is off, and a source below the repository's
root is refused.

A trim's `sparse` and `exclude` must be non-empty lists of strings,
`caller_scope_complete` a boolean and `trim_note` a string; an older
manifest's `"sparse": true` is now refused by name instead of crashing.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01NTnpjPjJj2aZy1Zk... (continued)

4085 of 4715 relevant lines covered (86.64%)

0.87 hits per line

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ID Job ID Ran Files Coverage
1 #3239.1 44
86.64
Source Files on build #3239