Story 1066 (merged 2026-05-14 23:39) introduced a periodic reconciler that
calls `reconcile_worktree_create` every 30 seconds (default
`reconcile_interval_secs`). The reconciler's docstring promises it is a no-op
for stories whose worktree already exists — but the implementation calls
`create_worktree`, whose reuse path was running `run_setup_commands`
unconditionally. Setup includes destructive `npm ci` (rm -rf node_modules
then reinstall), so every Coding story got `npm ci` fired every 30 seconds.
When story 1086 hit a gate-failure retry loop on 2026-05-15, the merge gate's
own `npm install`/`npm run build` raced one of these reconciler-driven
`npm ci` runs that was wiping node_modules — leaving `.bin/tsc` as a broken
symlink pointing into a half-populated `typescript/` package and producing
`sh: 1: tsc: not found`. 37 npm ci fires for 1086 in 5 hours against only
3 real Coding transitions, a 12x amplification driven entirely by the
30-second reconcile cadence.
Fix: align `create_worktree`'s behaviour with the contract `reconcile_worktree_create`
already documents — reuse is a no-op for setup commands. Sparse checkout
and `.mcp.json` rewrite still run (both cheap and idempotent).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Timmy
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