Add machine-readable JSON report (00BiocCheck.json)

[seandavi]

Motivation

BiocCheck results are currently only available as text. Anything that wants
to act on them — a CI gate, an editor, a bot that triages submissions — has to
parse 00BiocCheck.log, which is fragile and breaks whenever a message is
reworded.

Nearly everything needed is already collected internally: handleCondition()
records the originating check function via sys.call, handleCheck() records
the check title, and add() knows the severity. They are just flattened into
text at render time. This PR exposes them.

What this adds

Every run now writes 00BiocCheck.json next to 00BiocCheck.log in the
<PackageName>.BiocCheck folder:

{
  "metadata": { "Package": "MyPackage", "PackageVersion": "0.99.0", "...": "" },
  "summary": { "error": 1, "warning": 2, "note": 5 },
  "status": "error",
  "entries": [
    {
      "severity": "warning",
      "checkFun": "checkFormatting",
      "check": "Checking formatting of DESCRIPTION, NAMESPACE, ...",
      "message": "Consider shorter lines; 3 lines (1%) are > 80 characters long.",
      "help_text": "First few lines:",
      "details": ["R/foo.R#L12 x <- some_very_long_call( ..."],
      "locations": [ { "file": "R/foo.R", "line": 12 } ]
    }
  ],
  "text": ["* Checking formatting of DESCRIPTION, NAMESPACE, ...", "..."]
}

• summary / status give the tallies and the most severe condition
  (error, warning, note, or ok), so a gate is one line:
  jq -e '.summary.error == 0' MyPackage.BiocCheck/00BiocCheck.json
• entries has one record per condition raised. checkFun is the stable
  identifier to key on; check is the human-readable title, which is free to
  change between releases.
• locations are parsed inside BiocCheck from the two location formats the
  checks already emit (.lineReport and
  sprintf("%s (line %d, column %d)"), with or without a leading symbol
  name), so consumers never parse them. Chunk-relative vignette locations are
  deliberately omitted rather than reported as file lines.
• text is the log file, line for line — the JSON is a superset of the text
  report, nothing to cross-reference.

The same data is on the returned object: bc$getStatus(), bc$entries, and
bc$toJSON() (returns the JSON string when no file is given).

Implementation notes

• New entries field on the BiocCheck class, appended in add() and
  filtered in zero(). The existing log / composeReport / report text
  path is untouched, so there is no change to 00BiocCheck.log.
• toJSON / fromJSON were doubly encoding the payload (toJSON() to a
  string, then write_json() of that string) and are rewritten. They were not
  called anywhere in the package, so no on-disk format was in use.
• Field types are stable: details is always an array, help_text and
  locations are null when absent, metadata is always an object.
• jsonlite moves from Suggests to Imports. The alternative — an opt-in
  flag — would need to be set correctly in every CI job to be useful, and it
  is a small, dependency-free package. Happy to switch it to a dot-option if
  you would rather keep it optional.

Two judgment calls worth your review

1. The JSON is always written, with no opt-out (see above).
2. Four coding-practice checks reported bare file names (bad_coding.R) while
   every other check reports package-relative paths (R/bad_coding.R). They
   now use .getDirFiles() so locations.file resolves consistently. This
   changes existing text output, so it is easy to drop if you consider it
   out of scope.

Checklist

• Update the NEWS file
• Update the vignette file (new "Machine-readable output" section; also a
  short README section)
• Add unit tests — inst/tinytest/test_json.R, 36 assertions covering the
  schema, summary/status, both location formats, the round trip, and the
  files written by report()
• R CMD build & R CMD check — full local suite passes (221
  assertions); an end-to-end run on testpkg0 yields 49 entries matching
  13 errors / 17 warnings / 19 notes with 113 parsed locations

@LiNk-NY @lshep for review.

🤖 Generated with Claude Code

https://claude.ai/code/session_0153nSC2TGmUwxcXt8iCvweV

[codecov]

Codecov Report

❌ Patch coverage is 97.10145% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 70.06%. Comparing base (20f99c6) to head (4edf283).
⚠️ Report is 2 commits behind head on devel.

Files with missing lines	Patch %	Lines
R/BiocCheck-class.R	96.92%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #258      +/-   ##
==========================================
+ Coverage   69.17%   70.06%   +0.89%     
==========================================
  Files          15       15              
  Lines        3046     3117      +71     
==========================================
+ Hits         2107     2184      +77     
+ Misses        939      933       -6     

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