fix: batch — 12 cubic findings from PR #36

[four-bytes-robby]

Post-merge batch fix for 12 unresolved cubic findings from PR #36.

P1:

• batch-patch.ts: '' sentinel deletes valid empty files on rollback
• smart-patch.ts: mixed hunks lose context lines on splice

P2:

• smart-edit.ts: old_string not validated as non-empty
• solution-confidence.ts: run_tests result parsing missing guard
• solution-confidence.ts: score can exceed 1.0 via redistribution
• research.ts: query elements not validated as strings
• research.ts: scope not validated
• file-tree.ts: glob regex doesn't escape special chars
• tests/smart-patch.test.ts: 2x missing await on .rejects.toThrow()
• tests/file-tree.test.ts: missing await on .rejects.toThrow()

Docs:

• file-tree.ts: .gitignore claim in description, never implemented

[coderabbitai]

🔗 Related PRs

#15 - feat/14 append file tool [merged]
#20 - fix: correct after_line=-1 prepend position in append_file #16 [merged]
#24 - fix: align @typescript-eslint packages to 8.61.0 [merged]
#25 - feat: add gh_bot_review tool to parse AI bot findings #22 [merged]
#39 - fix: smart_edit — add output field, Claude-style diff, normalization typo #38 [merged]

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