Ai fixes+tests

.env

@@ -1,20 +1,5 @@
 # Source this file manually if you don't use direnv:
 #   source .env
-# Or add to your shell rc: source /path/to/git-cross/.env
-
-# Add cross wrapper to PATH
-export PATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd):$PATH"
-
-# Detect and add Homebrew to PATH
-if [ -d "/opt/homebrew/bin" ]; then
-    export PATH="/opt/homebrew/bin:$PATH"
-elif [ -d "/usr/local/bin" ]; then
-    export PATH="/usr/local/bin:$PATH"
-elif [ -d "/home/linuxbrew/.linuxbrew/bin" ]; then
-    export PATH="/home/linuxbrew/.linuxbrew/bin:$PATH"
-elif [ -n "$HOMEBREW_PREFIX" ]; then
-    export PATH="$HOMEBREW_PREFIX/bin:$PATH"
-fi
 
 export PATH="$HOME/bin:$PATH"
 

.envrc

@@ -1,3 +1,5 @@
-# .envrc – load environment variables for this repo
+# direnv - load environment variables for this repo
+source_up
+
 # If .env exists, source it (direnv will evaluate this file automatically)
 test -f "$(pwd)/.env" && source "$(pwd)/.env" || true

.github/workflows/ci.yml

@@ -2,9 +2,9 @@ name: CI
 
 on:
   push:
-    branches: [ main ]
+    branches: [ master, main ]
   pull_request:
-    branches: [ main ]
+    branches: [ master, main ]
 
 jobs:
   test:
@@ -22,11 +22,15 @@ jobs:
       run: |
         if [ "$RUNNER_OS" == "Linux" ]; then
           sudo apt-get update
-          sudo apt-get install -y fish rsync
+          sudo apt-get install -y fish rsync python3 jq
+          # Install yq
+          sudo wget https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64 -O /usr/bin/yq
+          sudo chmod +x /usr/bin/yq
+          # Install just
           curl --proto '=https' --tlsv1.2 -sSf https://just.systems/install.sh | bash -s -- --to ~/bin
           echo "$HOME/bin" >> $GITHUB_PATH
         elif [ "$RUNNER_OS" == "macOS" ]; then
-          brew install fish rsync just
+          brew install fish rsync just python3 jq yq
         fi
 
     - name: Verify installation
@@ -35,19 +39,23 @@ jobs:
         fish --version
         git --version
         rsync --version
+        python3 --version
+        jq --version
+        yq --version
 
     - name: Run dependency check
       run: just check-deps
 
     - name: Run all tests
-      run: ./test/test_all_commands.sh
+      run: just cross-test
 
     - name: Run individual tests
       run: |
         for test in test/test_*.sh; do
-          if [ -x "$test" ] && [ "$test" != "test/test_all_commands.sh" ]; then
-            echo "Running $test..."
-            $test
+          if [ -x "$test" ]; then
+            test_id=$(basename "$test" | sed 's/test_\([0-9]*\).*/\1/')
+            echo "Running test $test_id..."
+            just cross-test "$test_id" || echo "Test $test_id failed"
           fi
         done
 
@@ -62,11 +70,13 @@ jobs:
         TOTAL=0
         PASSED=0
 
+
         for test in test/test_*.sh; do
           if [ -x "$test" ]; then
             TOTAL=$((TOTAL + 1))
             TEST_NAME=$(basename "$test" .sh)
-            if $test > /dev/null 2>&1; then
+            test_id=$(echo "$TEST_NAME" | sed 's/test_\([0-9]*\).*/\1/')
+            if just cross-test "$test_id" > /dev/null 2>&1; then
               echo "| $TEST_NAME | ✅ PASS |" >> $GITHUB_STEP_SUMMARY
               PASSED=$((PASSED + 1))
             else

AGENTS.md

@@ -25,16 +25,61 @@
 
 ## Commands
 
-| Command | Purpose | Arguments |
-|---------|---------|-----------|
-| `use` | Add remote repository | `<name> <url>` |
-| `patch` | Vendor subdirectory | `<remote>:<path> <local> [branch]` |
-| `sync` | Update from upstream | None |
-| `list` | Show all patches | None |
-| `status` | Check patch status | None |
-| `diff-patch` | Compare local vs upstream | `[remote:path] [local]` (inferred) |
-| `push-upstream` | Push changes upstream | `[remote:path] [local]` (inferred) |
-| `replay` | Restore from Crossfile | None |
+All commands are accessible via `just cross <command>` or `./cross <command>` wrapper:
+
+### Core Workflow
+- **`use <name> <url>`** - Add a remote repository with branch auto-detection
+  - Auto-detects default branch (main/master) via `git ls-remote --symref`
+  - Fetches detected branch automatically
+  - Records in Crossfile
+
+- **`patch <remote:path[:branch]> <local_path> [branch]`** - Vendor a directory from remote
+  - Supports `remote:path:branch` syntax (branch in spec)
+  - Alternative: `remote:path local_path branch` (branch as 3rd arg)
+  - Creates worktree with sparse checkout
+  - Syncs to local path with rsync
+  - Creates intermediate directories automatically (`mkdir -p`)
+  - Updates Crossfile only on success (idempotency)
+
+- **`sync`** - Update all patches from upstream
+  - Updates all worktrees via git pull --rebase
+  - Checks for uncommitted changes in local paths
+  - Prompts before overwriting local modifications
+  - Executes `cross exec` commands from Crossfile
+
+- **`replay`** - Re-execute all Crossfile commands
+  - Processes each line sequentially
+  - Supports `cross` prefix and legacy format
+  - Skips comments and empty lines
+
+### Inspection
+- **`list`** - Show all configured patches in table format
+- **`status`** - Show patch status (diffs, upstream sync, conflicts)
+- **`diff [remote:path] [local_path]`** - Compare local vs upstream
+  - Auto-infers from current directory if in tracked path
+
+### Contribution
+- **`push [remote:path] [local_path]`** - Push changes back to upstream
+  - Syncs local to worktree
+  - Shows git status
+  - Interactive: Run (commit+push), Manual (subshell), Cancel
+  - Auto-infers from current directory if in tracked path
+
+### Automation
+- **`exec <command>`** - Execute arbitrary shell commands
+  - Used for post-hooks in Crossfile
+  - Can call user's Justfile recipes
+  - Example: `cross exec just posthook`
+
+### Utilities
+- **`help`** - Show usage and available commands
+- **`check-deps`** - Verify required dependencies (fish, rsync, git, python3, jq, yq)
+- **`setup`** - Auto-setup environment (direnv)
+
+### Internal Helpers
+- **`_resolve_context`** - Infer remote:path and local_path from CWD
+- **`_sync_from_crossfile`** - Process Crossfile for sync operations
+- **`update_crossfile`** - Append command to Crossfile (deduplicated)
 
 ## Testing