Merge branch 'main' into java-config-redesign

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: Ubuntu

.claude/hooks/post-edit-lint.sh

@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+# Everyone is on macOS so this should be fine, we don't account for Windows
+set -euo pipefail
+
+input=$(cat)
+file_path=$(echo "$input" | jq -r '.tool_input.file_path // empty')
+
+if [[ -z "$file_path" || ! -f "$file_path" ]]; then
+    exit 0
+fi
+
+if [[ "$file_path" == *.py ]]; then
+    # First run auto-fixes formatting; second run catches real lint errors
+    uv run prek --files "$file_path" 2>/dev/null || uv run prek --files "$file_path"
+fi

.claude/rules/code-style.md

@@ -11,5 +11,3 @@
 - **Paths**: Always use absolute paths
 - **Encoding**: Always pass `encoding="utf-8"` to `open()`, `read_text()`, `write_text()`, etc. in new or changed code — Windows defaults to `cp1252` which breaks on non-ASCII content. Don't flag pre-existing code that lacks it unless you're already modifying that line.
 - **Verification**: Use `uv run prek` to verify code — it handles ruff, ty, mypy in one pass. Don't run `ruff`, `mypy`, or `python -c "import ..."` separately; `prek` is the single verification command
-- **Pre-commit**: Run `uv run prek` before committing — fix any issues before creating the commit
-- **Pre-push**: Before pushing, run `uv run prek run --from-ref origin/<base>` to check all changed files against the PR base — this matches CI behavior and catches issues that per-commit prek misses. To detect the base branch: `gh pr view --json baseRefName -q .baseRefName 2>/dev/null || echo main`

.claude/rules/git.md

@@ -9,6 +9,8 @@
 - Commit message body should be concise (1-2 sentences max)
 - Merge for simple syncs, rebase when branches have diverged significantly
 - When committing to an external/third-party repo, follow that repo's own conventions for versioning, changelog, and CI
+- Pre-commit: Run `uv run prek` before committing — fix any issues before creating the commit
+- Pre-push: Run `uv run prek run --from-ref origin/<base>` to check all changed files against the PR base — this matches CI behavior and catches issues that per-commit prek misses. To detect the base branch: `gh pr view --json baseRefName -q .baseRefName 2>/dev/null || echo main`
 
 ## Pull Requests
 - PR titles should use conventional format

.claude/rules/workflow.md

@@ -0,0 +1,13 @@
+# Workflow
+
+## Code Changes
+- Before making any changes, outline your approach in 3-5 numbered steps. Include which repo/branch you'll work in, what commands you'll run, and what success looks like. Wait for approval before starting
+
+## Response Style
+- When listing items (PRs, functions, optimization targets), always provide the complete list ordered by priority on the first attempt. Do not give partial lists
+
+## Commands
+- When running long-running commands (benchmarks, profiling, optimizers like codeflash), always run them in the foreground. Do not use background processes
+
+## Debugging
+- When claiming something is a pre-existing issue (e.g., test failures on main), verify by checking out main and running the tests before making that claim

.claude/settings.json

@@ -0,0 +1,16 @@
+{
+  "hooks": {
+    "PostToolUse": [
+      {
+        "matcher": "Edit|Write",
+        "hooks": [
+          {
+            "type": "command",
+            "command": ".claude/hooks/post-edit-lint.sh",
+            "timeout": 30
+          }
+        ]
+      }
+    ]
+  }
+}

.gitignore

@@ -269,6 +269,8 @@ tessl.json
 # Claude Code - track shared rules, ignore local config
 .claude/*
 !.claude/rules/
+!.claude/settings.json
+!.claude/hooks/
 **/node_modules/**
 **/dist-nuitka/**
 **/.npmrc

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.15.0
+  rev: v0.15.8
   hooks:
     # Run the linter.
     - id: ruff-check

CLAUDE.md

@@ -10,13 +10,7 @@ CodeFlash is an AI-powered code optimizer that automatically improves performanc
 Discovery → Ranking → Context Extraction → Test Gen + Optimization → Baseline → Candidate Evaluation → PR
 ```
 
-1. **Discovery** (`discovery/`): Find optimizable functions across the codebase
-2. **Ranking** (`benchmarking/function_ranker.py`): Rank functions by addressable time using trace data
-3. **Context** (`languages/<lang>/context/`): Extract code dependencies (read-writable code + read-only imports)
-4. **Optimization** (`optimization/`, `api/`): Generate candidates via AI service, run in parallel with test generation
-5. **Verification** (`verification/`): Run candidates against tests, compare outputs via custom pytest plugin
-6. **Benchmarking** (`benchmarking/`): Measure performance, select best candidate by speedup
-7. **Result** (`result/`, `github/`): Create PR with winning optimization
+See `.claude/rules/architecture.md` for directory mapping and entry points.
 
 # Instructions
 - **Bug fix workflow** — follow these steps in order, do not skip ahead:

codeflash-java-runtime/build.gradle.kts

@@ -47,7 +47,12 @@ tasks.shadowJar {
     archiveVersion.set("1.0.0")
     archiveClassifier.set("")
 
-    relocate("org.objectweb.asm", "com.codeflash.asm")
+    relocate("org.objectweb.asm", "com.codeflash.shaded.org.objectweb.asm")
+    relocate("com.google.gson", "com.codeflash.shaded.com.google.gson")
+    relocate("com.esotericsoftware", "com.codeflash.shaded.com.esotericsoftware")
+    relocate("org.objenesis", "com.codeflash.shaded.org.objenesis")
+    relocate("org.slf4j", "com.codeflash.shaded.org.slf4j")
+    relocate("org.jacoco", "com.codeflash.shaded.org.jacoco")
 
     manifest {
         attributes(

codeflash-java-runtime/pom.xml

@@ -156,7 +156,35 @@
                             <relocations>
                                 <relocation>
                                     <pattern>org.objectweb.asm</pattern>
-                                    <shadedPattern>com.codeflash.asm</shadedPattern>
+                                    <shadedPattern>com.codeflash.shaded.org.objectweb.asm</shadedPattern>
+                                </relocation>
+                                <relocation>
+                                    <pattern>com.google.gson</pattern>
+                                    <shadedPattern>com.codeflash.shaded.com.google.gson</shadedPattern>
+                                </relocation>
+                                <relocation>
+                                    <pattern>com.esotericsoftware</pattern>
+                                    <shadedPattern>com.codeflash.shaded.com.esotericsoftware</shadedPattern>
+                                </relocation>
+                                <relocation>
+                                    <pattern>org.objenesis</pattern>
+                                    <shadedPattern>com.codeflash.shaded.org.objenesis</shadedPattern>
+                                </relocation>
+                                <relocation>
+                                    <pattern>org.slf4j</pattern>
+                                    <shadedPattern>com.codeflash.shaded.org.slf4j</shadedPattern>
+                                </relocation>
+                                <relocation>
+                                    <pattern>org.jacoco</pattern>
+                                    <shadedPattern>com.codeflash.shaded.org.jacoco</shadedPattern>
+                                </relocation>
+                                <relocation>
+                                    <pattern>org.kohsuke</pattern>
+                                    <shadedPattern>com.codeflash.shaded.org.kohsuke</shadedPattern>
+                                </relocation>
+                                <relocation>
+                                    <pattern>com.vladium</pattern>
+                                    <shadedPattern>com.codeflash.shaded.com.vladium</shadedPattern>
                                 </relocation>
                             </relocations>
                             <transformers>