chore: sync main into omni-java (batch 1/4)

.claude/rules/architecture.md

@@ -0,0 +1,28 @@
+# Architecture
+
+```
+codeflash/
+├── main.py                 # CLI entry point
+├── cli_cmds/               # Command handling, console output (Rich)
+├── discovery/              # Find optimizable functions
+├── context/                # Extract code dependencies and imports
+├── optimization/           # Generate optimized code via AI
+│   ├── optimizer.py        # Main optimization orchestration
+│   └── function_optimizer.py  # Per-function optimization logic
+├── verification/           # Run deterministic tests (pytest plugin)
+├── benchmarking/           # Performance measurement
+├── github/                 # PR creation
+├── api/                    # AI service communication
+├── code_utils/             # Code parsing, git utilities
+├── models/                 # Pydantic models and types
+├── languages/              # Multi-language support (Python, JavaScript/TypeScript)
+├── setup/                  # Config schema, auto-detection, first-run experience
+├── picklepatch/            # Serialization/deserialization utilities
+├── tracing/                # Function call tracing
+├── tracer.py               # Root-level tracer entry point for profiling
+├── lsp/                    # IDE integration (Language Server Protocol)
+├── telemetry/              # Sentry, PostHog
+├── either.py               # Functional Result type for error handling
+├── result/                 # Result types and handling
+└── version.py              # Version information
+```

.claude/rules/code-style.md

@@ -0,0 +1,9 @@
+# Code Style
+
+- **Line length**: 120 characters
+- **Python**: 3.9+ syntax
+- **Tooling**: Ruff for linting/formatting, mypy strict mode, prek for pre-commit checks
+- **Comments**: Minimal - only explain "why", not "what"
+- **Docstrings**: Do not add unless explicitly requested
+- **Naming**: NEVER use leading underscores (`_function_name`) - Python has no true private functions, use public names
+- **Paths**: Always use absolute paths, handle encoding explicitly (UTF-8)

.claude/rules/git.md

@@ -0,0 +1,6 @@
+# Git Commits & Pull Requests
+
+- Use conventional commit format: `fix:`, `feat:`, `refactor:`, `docs:`, `test:`, `chore:`
+- Keep commits atomic - one logical change per commit
+- Commit message body should be concise (1-2 sentences max)
+- PR titles should also use conventional format

.claude/rules/source-code.md

@@ -0,0 +1,11 @@
+---
+paths:
+  - "codeflash/**/*.py"
+---
+
+# Source Code Rules
+
+- Use `libcst` for code modification/transformation to preserve formatting. `ast` is acceptable for read-only analysis and parsing.
+- NEVER use leading underscores for function names (e.g., `_helper`). Python has no true private functions. Always use public names.
+- Any new feature or bug fix that can be tested automatically must have test cases.
+- If changes affect existing test expectations, update the tests accordingly. Tests must always pass after changes.

.claude/rules/testing.md

@@ -0,0 +1,15 @@
+---
+paths:
+  - "tests/**"
+  - "codeflash/**/*test*.py"
+---
+
+# Testing Conventions
+
+- Code context extraction and replacement tests must always assert for full string equality, no substring matching.
+- Use pytest's `tmp_path` fixture for temp directories (it's a `Path` object).
+- Write temp files inside `tmp_path`, never use `NamedTemporaryFile` (causes Windows file contention).
+- Always call `.resolve()` on Path objects to ensure absolute paths and resolve symlinks.
+- Use `.as_posix()` when converting resolved paths to strings (normalizes to forward slashes).
+- Any new feature or bug fix that can be tested automatically must have test cases.
+- If changes affect existing test expectations, update the tests accordingly. Tests must always pass after changes.

.github/workflows/claude.yml

@@ -54,20 +54,34 @@ jobs:
             PR NUMBER: ${{ github.event.pull_request.number }}
             EVENT: ${{ github.event.action }}
 
-            ## STEP 1: Run pre-commit checks and fix issues
+            ## STEP 1: Run prek and mypy checks, fix issues
 
-            First, run `uv run prek run --from-ref origin/main` to check for linting/formatting issues on files changed in this PR.
+            First, run these checks on files changed in this PR:
+            1. `uv run prek run --from-ref origin/main` - linting/formatting issues
+            2. `uv run mypy <changed_files>` - type checking issues
 
-            If there are any issues:
+            If there are prek issues:
             - For SAFE auto-fixable issues (formatting, import sorting, trailing whitespace, etc.), run `uv run prek run --from-ref origin/main` again to auto-fix them
+            - For issues that prek cannot auto-fix, do NOT attempt to fix them manually — report them as remaining issues in your summary
+
+            If there are mypy issues:
+            - Fix type annotation issues (missing return types, Optional/None unions, import errors for type hints, incorrect types)
+            - Do NOT add `type: ignore` comments - always fix the root cause
+
+            After fixing issues:
             - Stage the fixed files with `git add`
-            - Commit with message "style: auto-fix linting issues"
+            - Commit with message "style: auto-fix linting issues" or "fix: resolve mypy type errors" as appropriate
             - Push the changes with `git push`
 
+            IMPORTANT - Verification after fixing:
+            - After committing fixes, run `uv run prek run --from-ref origin/main` ONE MORE TIME to verify all issues are resolved
+            - If errors remain, either fix them or report them honestly as unfixed in your summary
+            - NEVER claim issues are fixed without verifying. If you cannot fix an issue, say so
+
             Do NOT attempt to fix:
-            - Type errors that require logic changes
-            - Complex refactoring suggestions
-            - Anything that could change behavior
+            - Type errors that require logic changes or refactoring
+            - Complex generic type issues
+            - Anything that could change runtime behavior
 
             ## STEP 2: Review the PR
 
@@ -85,7 +99,6 @@ jobs:
             - Only create NEW inline comments for HIGH-PRIORITY issues found in changed files.
             - Limit to 5-7 NEW comments maximum per review.
             - Use CLAUDE.md for project-specific guidance.
-            - Use `gh pr comment` for summary-level feedback.
             - Use `mcp__github_inline_comment__create_inline_comment` sparingly for critical code issues only.
 
             ## STEP 3: Coverage analysis
@@ -122,7 +135,45 @@ jobs:
             - New implementations/files: Must have ≥75% test coverage
             - Modified code: Changed lines should be exercised by existing or new tests
             - No coverage regressions: Overall coverage should not decrease
-          claude_args: '--allowedTools "mcp__github_inline_comment__create_inline_comment,Bash(gh pr comment:*),Bash(gh pr diff:*),Bash(gh pr view:*),Bash(gh pr list:*),Bash(gh issue view:*),Bash(gh issue list:*),Bash(gh api:*),Bash(uv run prek *),Bash(uv run coverage *),Bash(uv run pytest *),Bash(git status*),Bash(git add *),Bash(git commit *),Bash(git push*),Bash(git diff *),Bash(git checkout *),Read,Glob,Grep"'
+
+            ## STEP 4: Post ONE consolidated summary comment
+
+            CRITICAL: You must post exactly ONE summary comment containing ALL results (pre-commit, review, coverage).
+            DO NOT post multiple separate comments. Use this format:
+
+            ```
+            ## PR Review Summary
+
+            ### Prek Checks
+            [status and any fixes made]
+
+            ### Code Review
+            [critical issues found, if any]
+
+            ### Test Coverage
+            [coverage table and analysis]
+
+            ---
+            *Last updated: <timestamp>*
+            ```
+
+            To ensure only ONE comment exists:
+            1. Find existing claude[bot] comment: `gh api repos/${{ github.repository }}/issues/${{ github.event.pull_request.number }}/comments --jq '.[] | select(.user.login == "claude[bot]") | .id' | head -1`
+            2. If found, UPDATE it: `gh api --method PATCH repos/${{ github.repository }}/issues/comments/<ID> -f body="<content>"`
+            3. If not found, CREATE: `gh pr comment ${{ github.event.pull_request.number }} --body "<content>"`
+            4. Delete any OTHER claude[bot] comments to clean up duplicates: `gh api repos/${{ github.repository }}/issues/${{ github.event.pull_request.number }}/comments --jq '.[] | select(.user.login == "claude[bot]") | .id' | tail -n +2 | xargs -I {} gh api --method DELETE repos/${{ github.repository }}/issues/comments/{}`
+
+            ## STEP 5: Merge pending codeflash optimization PRs
+
+            Check for open optimization PRs from codeflash and merge if CI passes:
+
+            1. List open PRs from codeflash bot:
+               `gh pr list --author "codeflash-ai[bot]" --state open --json number,title,headRefName`
+
+            2. For each optimization PR:
+               - Check if CI is passing: `gh pr checks <number>`
+               - If all checks pass, merge it: `gh pr merge <number> --squash --delete-branch`
+          claude_args: '--model claude-opus-4-6 --allowedTools "mcp__github_inline_comment__create_inline_comment,Bash(gh pr comment:*),Bash(gh pr diff:*),Bash(gh pr view:*),Bash(gh pr list:*),Bash(gh pr checks:*),Bash(gh pr merge:*),Bash(gh issue view:*),Bash(gh issue list:*),Bash(gh api:*),Bash(uv run prek *),Bash(uv run mypy *),Bash(uv run coverage *),Bash(uv run pytest *),Bash(git status*),Bash(git add *),Bash(git commit *),Bash(git push*),Bash(git diff *),Bash(git checkout *),Read,Glob,Grep,Edit"'
           additional_permissions: |
             actions: read
         env:
@@ -194,7 +245,7 @@ jobs:
         uses: anthropics/claude-code-action@v1
         with:
           use_foundry: "true"
-          claude_args: '--allowedTools "Read,Edit,Write,Glob,Grep,Bash(git status*),Bash(git diff*),Bash(git add *),Bash(git commit *),Bash(git push*),Bash(git log*),Bash(git merge*),Bash(git fetch*),Bash(git checkout*),Bash(git branch*),Bash(uv run prek *),Bash(prek *),Bash(uv run ruff *),Bash(uv run pytest *),Bash(uv run mypy *),Bash(uv run coverage *),Bash(gh pr comment*),Bash(gh pr view*),Bash(gh pr diff*),Bash(gh pr merge*),Bash(gh pr close*)"'
+          claude_args: '--model claude-opus-4-6 --allowedTools "Read,Edit,Write,Glob,Grep,Bash(git status*),Bash(git diff*),Bash(git add *),Bash(git commit *),Bash(git push*),Bash(git log*),Bash(git merge*),Bash(git fetch*),Bash(git checkout*),Bash(git branch*),Bash(uv run prek *),Bash(prek *),Bash(uv run ruff *),Bash(uv run pytest *),Bash(uv run mypy *),Bash(uv run coverage *),Bash(gh pr comment*),Bash(gh pr view*),Bash(gh pr diff*),Bash(gh pr merge*),Bash(gh pr close*)"'
           additional_permissions: |
             actions: read
         env:

.gitignore

@@ -264,6 +264,10 @@ WARP.MD
 .mcp.json
 .tessl/
 tessl.json
+
+# Claude Code - track shared rules, ignore local config
+.claude/*
+!.claude/rules/
 **/node_modules/**
 **/dist-nuitka/**
 **/.npmrc

CLAUDE.md

@@ -24,64 +24,15 @@ uv run mypy codeflash/           # Type check
 uv run ruff check codeflash/     # Lint
 uv run ruff format codeflash/    # Format
 
-# Pre-commit (run before committing)
-uv run pre-commit run --all-files
+# Linting (run before committing)
+uv run prek run --from-ref origin/main
 
 # Running the CLI
 uv run codeflash --help
 uv run codeflash init            # Initialize in a project
 uv run codeflash --all           # Optimize entire codebase
 ```
 
-## Architecture
-
-```
-codeflash/
-├── main.py                 # CLI entry point
-├── cli_cmds/               # Command handling, console output (Rich)
-├── discovery/              # Find optimizable functions
-├── context/                # Extract code dependencies and imports
-├── optimization/           # Generate optimized code via AI
-│   ├── optimizer.py        # Main optimization orchestration
-│   └── function_optimizer.py  # Per-function optimization logic
-├── verification/           # Run deterministic tests (pytest plugin)
-├── benchmarking/           # Performance measurement
-├── github/                 # PR creation
-├── api/                    # AI service communication
-├── code_utils/             # Code parsing, git utilities
-├── models/                 # Pydantic models and types
-├── tracing/                # Function call tracing
-├── lsp/                    # IDE integration (Language Server Protocol)
-├── telemetry/              # Sentry, PostHog
-├── either.py               # Functional Result type for error handling
-└── result/                 # Result types and handling
-```
-
-### Key Rules to follow
-
-- Use libcst, not ast - For Python, always use `libcst` for code parsing/modification to preserve formatting.
-- Code context extraction and replacement tests must always assert for full string equality, no substring matching.
-- Any new feature or bug fix that can be tested automatically must have test cases.
-- If changes affect existing test expectations, update the tests accordingly. Tests must always pass after changes.
-- NEVER use leading underscores for function names (e.g., `_helper`). Python has no true private functions. Always use public names.
-
-## Code Style
-
-- **Line length**: 120 characters
-- **Python**: 3.9+ syntax
-- **Tooling**: Ruff for linting/formatting, mypy strict mode, pre-commit hooks
-- **Comments**: Minimal - only explain "why", not "what"
-- **Docstrings**: Do not add unless explicitly requested
-- **Naming**: NEVER use leading underscores (`_function_name`) - Python has no true private functions, use public names
-- **Paths**: Always use absolute paths, handle encoding explicitly (UTF-8)
-
-## Git Commits & Pull Requests
-
-- Use conventional commit format: `fix:`, `feat:`, `refactor:`, `docs:`, `test:`, `chore:`
-- Keep commits atomic - one logical change per commit
-- Commit message body should be concise (1-2 sentences max)
-- PR titles should also use conventional format
-
 <!-- Section below is auto-generated by `tessl install` - do not edit manually -->
 
 # Agent Rules <!-- tessl-managed -->

MULTI_LANGUAGE_ARCHITECTURE.md

@@ -386,7 +386,7 @@ class JavaScriptTransformer:
 
 from pathlib import Path
 from codeflash.languages.base import LanguageSupport, FunctionInfo, CodeContext
-from codeflash.languages.treesitter_utils import TreeSitterAnalyzer
+from codeflash.languages.javascript.treesitter import TreeSitterAnalyzer
 from codeflash.languages.javascript.transformer import JavaScriptTransformer
 
 class JavaScriptSupport(LanguageSupport):
@@ -523,7 +523,7 @@ class JavaScriptSupport(LanguageSupport):
 # codeflash/languages/javascript/test_discovery.py
 
 from pathlib import Path
-from codeflash.languages.treesitter_utils import TreeSitterAnalyzer
+from codeflash.languages.javascript.treesitter import TreeSitterAnalyzer
 
 class JestTestDiscovery:
     """Static analysis-based test discovery for Jest."""

codeflash/api/aiservice.py

@@ -841,6 +841,7 @@ def get_optimization_review(
         replay_tests: str,
         calling_fn_details: str,
         language: str = "python",
+        **_kwargs: Any,
     ) -> OptimizationReviewResult:
         """Compute the optimization review of current Pull Request.
 

codeflash/api/cfapi.py

@@ -285,6 +285,7 @@ def create_staging(
     optimization_review: str = "",
     original_line_profiler: str | None = None,
     optimized_line_profiler: str | None = None,
+    **_kwargs: Any,  # ignores the language argument TODO Hesham: staging for all langs
 ) -> Response:
     """Create a staging pull request, targeting the specified branch. (usually 'staging').
 

codeflash/cli_cmds/cli.py

@@ -10,7 +10,7 @@
 from codeflash.cli_cmds.console import logger
 from codeflash.cli_cmds.extension import install_vscode_extension
 from codeflash.code_utils import env_utils
-from codeflash.code_utils.code_utils import exit_with_message
+from codeflash.code_utils.code_utils import exit_with_message, normalize_ignore_paths
 from codeflash.code_utils.config_parser import parse_config_file
 from codeflash.languages.test_framework import set_current_test_framework
 from codeflash.lsp.helpers import is_LSP_enabled
@@ -296,16 +296,12 @@ def process_pyproject_config(args: Namespace) -> Namespace:
 
             require_github_app_or_exit(owner, repo_name)
 
-    if hasattr(args, "ignore_paths") and args.ignore_paths is not None:
-        normalized_ignore_paths = []
-        for path in args.ignore_paths:
-            path_obj = Path(path)
-            if path_obj.exists():
-                normalized_ignore_paths.append(path_obj.resolve())
-            # Silently skip non-existent paths (e.g., .next, dist before build)
-        args.ignore_paths = normalized_ignore_paths
     # Project root path is one level above the specified directory, because that's where the module can be imported from
     args.module_root = Path(args.module_root).resolve()
+    if hasattr(args, "ignore_paths") and args.ignore_paths is not None:
+        # Normalize ignore paths, supporting both literal paths and glob patterns
+        # Use module_root as base path for resolving relative paths and patterns
+        args.ignore_paths = normalize_ignore_paths(args.ignore_paths, base_path=args.module_root)
     # If module-root is "." then all imports are relatives to it.
     # in this case, the ".." becomes outside project scope, causing issues with un-importable paths
     args.project_root = project_root_from_module_root(args.module_root, pyproject_file_path)

codeflash/cli_cmds/init_javascript.py

@@ -154,6 +154,32 @@ def determine_js_package_manager(project_root: Path) -> JsPackageManager:
     return JsPackageManager.UNKNOWN
 
 
+def find_node_modules_with_package(project_root: Path, package_name: str) -> Path | None:
+    """Find node_modules directory containing a specific package.
+
+    Searches from project_root up to filesystem root for node_modules containing
+    the specified package. This supports monorepo setups where dependencies are
+    hoisted to the workspace root.
+
+    Args:
+        project_root: Starting directory for the search.
+        package_name: Name of the package to look for (e.g., "jest", "vitest").
+
+    Returns:
+        Path to the node_modules directory containing the package, or None if not found.
+
+    """
+    current_dir = project_root.resolve()
+    while current_dir != current_dir.parent:
+        node_modules = current_dir / "node_modules"
+        if node_modules.exists():
+            package_path = node_modules / package_name
+            if package_path.exists():
+                return node_modules
+        current_dir = current_dir.parent
+    return None
+
+
 def get_package_install_command(project_root: Path, package: str, dev: bool = True) -> list[str]:
     """Get the correct install command for the project's package manager.
 

codeflash/code_utils/code_extractor.py

@@ -1772,7 +1772,7 @@ def _extract_calling_function_js(source_code: str, function_name: str, ref_line:
 
     """
     try:
-        from codeflash.languages.treesitter_utils import TreeSitterAnalyzer, TreeSitterLanguage
+        from codeflash.languages.javascript.treesitter import TreeSitterAnalyzer, TreeSitterLanguage
 
         # Try TypeScript first, fall back to JavaScript
         for lang in [TreeSitterLanguage.TYPESCRIPT, TreeSitterLanguage.TSX, TreeSitterLanguage.JAVASCRIPT]: