#42 fix: batch — 12 cubic findings from PR #36 + file-tree hardening #40

Summary

Post-merge batch fix for 12 cubic-dev-ai findings from PR #36, plus additional file-tree tool hardening.

Fixed (12 cubic findings)

#	Finding	Status
1	batch-patch.ts: '' sentinel deletes valid empty files on rollback	✅ Fixed
2	smart-patch.ts: mixed hunks lose context lines on splice	✅ Fixed
3	smart-edit.ts: old_string not validated as non-empty	✅ Fixed
4	solution-confidence.ts: run_tests result parsing missing guard	✅ Fixed
5	solution-confidence.ts: score can exceed 1.0 via redistribution	✅ Fixed
6	research.ts: query elements not validated as strings	✅ Already validated
7	research.ts: scope not validated	✅ Already validated
8	file-tree.ts: glob regex doesn't escape special chars	✅ Fixed
9	tests/smart-patch.test.ts: 2x missing await	✅ Fixed
10	tests/file-tree.test.ts: missing await	✅ Fixed
11	file-tree.ts: .gitignore claim in description	✅ Fixed (removed claim)

Additional file-tree hardening

• Removed .gitignore dead-code special-casing
• Unified metadata shape: single files now return metadata.tree (not metadata.entries)
• Added symlink cycle protection (use lstatSync, skip symlinks)
• Made SKIP_DIRS unconditional (.git never shown, even with include_hidden: true)
• Added 5 new tests: filter, depth, hidden files, symlinks, single-file metadata

Test results

• 110/111 tests pass (1 pre-existing lsp-hover timeout, unrelated)
• Lint clean on all changed files

Closes #40

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Summary by cubic

Batch fixes for 12 findings from PR #36 and hardens the file-tree tool for safer, more consistent output. Addresses #40.

• Bug Fixes

  • batch-patch: atomic rollback no longer deletes valid empty files (tracks non-existent files as null).
  • smart-patch: preserve context lines; replace only deletions when applying hunks.
  • smart-edit: require non-empty old_string.
  • solution-confidence: guard test result parsing; cap redistributed score at 1.0.
  • file-tree: escape glob patterns; use lstat and skip symlinks; always skip .git, node_modules, vendor; remove .gitignore special-casing; single-file metadata now uses metadata.tree.
  • tests: add cases for filter, depth, hidden files (default off, opt-in via include_hidden), symlinks, and single-file metadata.

• Migration

  • If you read single-file results, switch from metadata.entries to metadata.tree.
  • .git is always skipped, even with include_hidden: true; symlinked dirs are ignored.

Summary by CodeRabbit

• Bug Fixes

  • Symbolic links are now properly skipped during directory traversal to prevent cycles
  • Glob pattern filtering now correctly handles special characters in filter expressions

• Improvements

  • Consistent hidden file handling: dot-prefixed entries are uniformly excluded when hidden files are not requested
  • Enhanced support for directory depth limiting