What happened?

Two related issues hit on a fresh fallow init --hooks against a Husky-using repo:

$ fallow init --hooks
Error: .husky/pre-commit already exists. Add the following line to your existing hook:

  fallow dead-code --changed-since <base> --fail-on-issues --quiet

1. Why only dead-code and not fallow audit?

crates/cli/src/init.rs hard-codes a single command in both the generated script and the "already exists" error message:

fallow dead-code --changed-since {base_ref} --fail-on-issues --quiet

But fallow audit already exists, takes --changed-since + --fail-on-issues, and bundles all three analyses (dead-code + dupes + health) into one verdict. Is audit deliberately excluded from pre-commit (too slow / too noisy on partial diffs?) or is this a doc/CLI gap? Either way, docs.fallow.tools/cli/init doesn't say.

2. The base ref is baked in at install time

The auto-detected (or --branch-supplied) ref is format!'d literally into the shell script:

fallow dead-code --changed-since main --fail-on-issues --quiet

That works for a feature → main topology. It breaks on any repo with multiple long-lived integration branches (next-release / hotfix / LTS), because the right base depends on which integration branch the feature targets — not on the global default sampled at hook-install time. Concrete failure modes:

• Hotfix branched off a non-default integration branch → hook diffs against the wrong base, producing false positives (code "missing" on default) or false negatives.
• No way to say "diff against the merge-base with my upstream" (git merge-base @{upstream} HEAD), which is the topology-agnostic answer.

Combined ask

1. Document why dead-code (not audit) is the recommended pre-commit gate, or add --hooks-command audit.

2. Have the generated hook resolve the base ref at commit time rather than baking it in, e.g.:

   UPSTREAM="$(git rev-parse --abbrev-ref --symbolic-full-name @{upstream} 2>/dev/null || true)"
   BASE="${UPSTREAM#*/}"
   fallow dead-code --changed-since "${BASE:-main}" --fail-on-issues --quiet

Reproduction

mkdir -p /tmp/fallow-init-hooks-repro && cd /tmp/fallow-init-hooks-repro
git init -q && git -c user.email=a@b -c user.name=a commit --allow-empty -qm init
mkdir -p .husky && echo '#!/bin/sh' > .husky/pre-commit && chmod +x .husky/pre-commit

# 1. Hook installer only suggests dead-code, never audit:
fallow init --hooks
# => Error: .husky/pre-commit already exists. Add the following line ...
#      fallow dead-code --changed-since main --fail-on-issues --quiet

# 2. --branch is baked in literally; switching feature branches later doesn't change it:
rm .husky/pre-commit
fallow init --hooks --branch develop
grep fallow .husky/pre-commit
# => fallow dead-code --changed-since develop --fail-on-issues --quiet

Expected behavior

Either documented or implemented:

• Doc explains the dead-code-vs-audit choice and the recommended setup for repos with multiple integration branches; or
• fallow init --hooks resolves the base ref at hook execution time (e.g. via @{upstream}); or
• fallow init --hooks --hooks-command audit opt-in to scaffold fallow audit instead of fallow dead-code.

Fallow version

2.56.0

Operating system

macOS

Configuration

No `.fallowrc.json` / `fallow.toml` is required to reproduce — the issue is in the hook scaffolder itself, not in analysis configuration.