repo-native-alignment: Agent for Claude Code

/worktree-setup

Bootstrap RNA in a git worktree so code navigation is fast and correct from the first tool call.

Invoke this skill at the start of any session that runs inside a worktree (i.e., when git worktree list shows more than one entry and the cwd is not the main checkout).

You are an RNA power user. Use RNA MCP tools (search, repo_map, outcome_progress, list_roots) for all code navigation — never Grep or Read for code understanding. Every Grep/Read instead of an RNA tool is a friction event. Log it with /friction.

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Quick setup (TL;DR)

# 1. Scan (fast — warm cache via prep-worktree.sh already ran)
repo-native-alignment scan --repo . 2>&1 | tail -2

# 2. Verify index is live
COUNT=$(repo-native-alignment search "" --repo . --limit 1 2>/dev/null | grep -o "[0-9]* symbols" | head -1)
echo "RNA: $COUNT indexed"
# If COUNT is 0 or missing → run full scan and investigate (see Step 2 below)

# 3. Navigate with RNA — never Grep/Read for code
mcp__rna-mcp__repo_map     # orientation
mcp__rna-mcp__search       # symbol / semantic search

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Full process

Step 1: Scan the worktree

The worktree's .oh/.cache/ was seeded from the main repo's cache by scripts/prep-worktree.sh. The first scan is an incremental pass — it only re-indexes files that changed since the cache was copied.

repo-native-alignment scan --repo . 2>&1 | tail -2

Expected output (warm cache):

Scanned 312 files in 14s (12 changed, 300 cached)
Index ready.

If the script hasn't been run yet (cold start), run a full scan:

repo-native-alignment scan --repo . --full 2>&1 | tail -2

Full scans take 30–60 s for a typical Rust repo. Warm incremental scans take ~15 s.

Step 2: Verify the index is live

COUNT=$(repo-native-alignment search "" --repo . --limit 1 2>/dev/null | grep -o "[0-9]* symbols" | head -1)
echo "RNA: $COUNT indexed"

If COUNT is 0 or the command errors:

1. Run a forced full scan:

   repo-native-alignment scan --repo . --full 2>&1
   

2. Verify the binary is on $PATH:

   which repo-native-alignment 2>/dev/null \
     || ls target/release/repo-native-alignment 2>/dev/null \
     || ls target/debug/repo-native-alignment 2>/dev/null
   

3. Check that --repo . resolves to the worktree root (not the main checkout).