Fix worktree mode filtering out all diff-discovered functions

[KRRT7]

Summary

• In --worktree mode (git-diff path), get_git_diff resolves file paths from cwd (the original repo), but module_root/project_root have been mirrored to the worktree directory by mirror_paths_for_worktree_mode. This caused filter_functions to reject all diff-discovered functions as "outside module-root" since the paths are in different directory trees.
• Fix uses pre-mirror roots for filtering, then remaps the discovered file paths to the worktree for downstream optimization.

Test plan

• Verified codeflash --worktree now finds functions (previously reported "Found 0 function to optimize" with "Functions outside module-root: 1")
• Verify --all and --file modes are unaffected (guarded by condition)

[claude]

PR Review Summary

Prek Checks

✅ All checks pass — ruff check and ruff format both passed with no issues.

Mypy

⚠️ 167 mypy errors reported across the two changed files, but all are pre-existing (same union-attr, type-arg, and other patterns that exist on main). No new type errors introduced by this PR.

Code Review

✅ No critical issues found. The changes are logically sound:

• optimizer.py: In worktree mode with git-diff discovery, uses original (non-worktree) project_root/module_root for function discovery so path comparisons match, then remaps discovered file paths to the worktree via mirror_path + dataclasses.replace. The guard condition (use_original_roots) correctly checks for worktree mode and excludes --all/--file modes.
• function_optimizer.py: Resolves git root from module_root (via GitRepo) instead of defaulting to cwd, fixing PR creation in worktree mode where cwd may not be inside the worktree.

Minor nit: Path(file_path) on line 223 of optimizer.py is redundant since file_path is already a Path (dict key type), but harmless.

Test Coverage

File	Main	PR	Δ
codeflash/optimization/function_optimizer.py	18% (1162 stmts)	18% (1163 stmts)	0%
codeflash/optimization/optimizer.py	20% (411 stmts)	20% (430 stmts)	0%
Total	19%	19%	0%

Changed lines coverage:

• optimizer.py lines 186-232 (new worktree remapping logic): Not covered by tests. The original get_functions_to_optimize call path was also uncovered on main.
• function_optimizer.py lines 2226, 2230 (git root resolution change): Not covered. The original git_root_dir() calls at these lines were also uncovered on main.

Assessment: No coverage regression. The new code follows the same integration-heavy code paths that were already uncovered. These paths involve git worktree operations that are difficult to unit test without integration infrastructure.

Test results: 2374 passed, 57 skipped, 8 failed (all failures in test_tracer.py, pre-existing and unrelated to this PR).

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Last updated: 2026-02-18