lint-staged repeats repository-wide checks for each chunk on large merge commits

## Problem

A large merge commit causes `lint-staged.config.ts` to schedule `pnpm lint` separately for each staged-file chunk. Those commands each lint the entire repository, so argument chunking does not bound the expensive work and can run duplicate full scans concurrently.

## Evidence

Observed while integrating main `dab829a54b` into #16177 on macOS arm64, Node 26.8.2 / pnpm 11.13.1. The normal pre-commit output reports two 669-file task groups and two `[STARTED] pnpm lint` entries after separate formatter chunks. Both commands are identical repository-wide checks. No hook was disabled.

`lintCommands()` selects `pnpm lint` whenever the chunk has more than 10 code/style files. `typecheckCommands()` also returns repository-wide checks from the per-chunk configuration; verify and deduplicate those as part of the fix.

## Expected result

Run applicable repository-wide gates once per commit, while retaining safe argument chunking for file-scoped formatting/lint. Preserve every required gate and the failure exit status. Validate the command plan with a staged-file set large enough to cross the chunk threshold.

Related: #14788 discussed lint coverage and large-merge resource pressure. This issue specifically tracks repeated repository-wide scheduling; it is deferred from the Agent consent PR to keep that change scoped.

Start in lint-staged.config.ts, tracing lintCommands() and typecheckCommands() for a staged-file set large enough to cross the chunk threshold. Validate the command plan against the reported duplicate pnpm lint entries, then confirm repository-wide gates run once, file-scoped checks remain chunked, and failures preserve their exit status.

Written by the indexing model from the issue text.