feat(pipeline): add hidden --pool-scheduler override for A/B benchmarking

[nh13]

#941 has merged, so this PR is rebased onto main and now contains a single commit: the new --pool-scheduler flag. (The earlier perf(group,dedup,clip) commit was a duplicate of what shipped in #941 and has been dropped.)

Why

The chain engine picks the pool dispatch scheduler per chain — drain-first for terminal group/dedup/clip and a BAM sort source, upstream-first otherwise. Validating that choice, or measuring whether an as-yet-unenabled command would benefit, meant building two binaries. This adds a runtime knob to A/B the tuning on any command from one build.

What

A hidden --pool-scheduler <auto|drain-first|chain-order> on the shared SchedulerOptions (flattened into every chain command, cloned into ChainSpec), so it reaches ChainBuilder::build with no per-command wiring:

• auto (default) — automatic per-chain decision; no behavior change.
• drain-first / chain-order — force one direction on every chain.

build() resolves it through a pure, unit-tested resolve_use_drain_first(override, auto) and emits a warn! when it overrides the automatic choice, so a benchmark records that a non-default scheduler ran. Value names match the --pipeline-stats scheduler names.

• Hidden (hide = true); distinct from the legacy, chain-unwired --scheduler strategy flag.
• Coverage: rides on SchedulerOptions, so it reaches extract, copy-umi, correct, align, group, simplex, duplex, codec, clip, filter, dedup, retag. It does not reach sort, zipper, fastq, downsample (they don't flatten SchedulerOptions) — notably sort is drain-first but not overridable via this flag. Worth a follow-up if we want full coverage.

What it already found (empirical sweep, this flag, 60M-class inputs, t8, tight reps)

command	Δ drain-first vs chain-order	note
group / dedup / clip	−6 … −14%	shipped in #941 (output verified)
retag	−4.9%	helps — candidate
simplex / codec	−3.0 … −3.5%	helps (modest) — candidate
extract	+459% (5.6× slower)	FASTQ source starved by downstream-first — must stay chain-order

Takeaway: drain-first is not universally safe and not reliably predictable from chain shape — most commands modestly benefit, but a source-bound command (extract) is catastrophically hurt. Per-command measurement is mandatory, which is what this flag is for. Only the confirmed strong, output-identical winners (group/dedup/clip) are enabled by default (shipped in #941).

Testing

• resolve_use_drain_first_matrix — 6-case rstest over the override × auto matrix.
• pool_scheduler_override_warning_matrix — 6-case rstest over the warning message selection.
• End-to-end: hidden from --help; rejects bogus values; group --pool-scheduler chain-order logs "forcing upstream-first"; retag --pool-scheduler drain-first logs "forcing downstream-first"; plain runs log nothing.
• cargo ci-fmt/ci-lint clean; existing SchedulerOptions unit tests updated for the new field.

Usage: <cmd> --pool-scheduler drain-first vs --pool-scheduler chain-order (same input/build) is a clean A/B; add --pipeline-stats to correlate.

Risk: output changes none; unsafe changes none and no CLAUDE.md allowlist update applies; memory bounds, queue capacity, and thread/backpressure policy changes none.

• Adds hidden --pool-scheduler <auto|drain-first|chain-order> support.
• Propagates the override through ChainSpec to ChainBuilder::build.
• Preserves automatic scheduling by default.
• Logs a warning when a forced mode changes the automatic choice.
• Adds resolution, validation, help visibility, warning, and default-behavior tests.

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Walkthrough

The change adds a hidden --pool-scheduler option with automatic, drain-first, and chain-order modes. The chain builder resolves the selected mode and logs warnings for contradictory overrides. Tests cover scheduler resolution and warning behavior.

Changes

Pool scheduler selection

Layer / File(s)	Summary
Scheduler option contract src/lib/commands/common.rs	Adds the PoolScheduler enum, stores the hidden CLI setting in SchedulerOptions, exposes an accessor, and updates test fixtures to use Auto.
Chain dispatch resolution src/lib/pipeline/chains/builder.rs	Resolves automatic or explicit scheduler modes and logs warnings when an override contradicts the automatic choice. Parameterized tests cover resolution and warning behavior.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Merge Risk: ⚪ Minimal · up to 8fefc

This adds a hidden benchmarking override for pool scheduling while retaining the existing automatic behavior by default. No current merge-blocking risk remains.

Sequence Diagram(s)

sequenceDiagram
  participant CLI
  participant SchedulerOptions
  participant ChainBuilder
  CLI->>SchedulerOptions: Parse --pool-scheduler
  SchedulerOptions->>ChainBuilder: Provide pool_scheduler()
  ChainBuilder->>ChainBuilder: Resolve automatic or explicit direction
  ChainBuilder-->>CLI: Log contradictory override warning when applicable

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🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title follows the required Conventional Commit format. It uses the valid type feat, the relevant pipeline scope, a lowercase imperative description, and no trailing period. It accurately descr…
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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Codecov Report

❌ Patch coverage is 94.59459% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.43%. Comparing base (a54a17e) to head (8fefc12).

Files with missing lines	Patch %	Lines
src/lib/pipeline/chains/builder.rs	93.33%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #942      +/-   ##
==========================================
- Coverage   94.44%   94.43%   -0.02%     
==========================================
  Files         307      307              
  Lines      151152   151188      +36     
==========================================
+ Hits       142763   142777      +14     
- Misses       8389     8411      +22     

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Actionable comments posted: 1

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Inline comments:
In `@src/lib/pipeline/chains/builder.rs`:
- Around line 492-495: Correct the scheduler documentation in
src/lib/pipeline/chains/builder.rs at lines 492-495 by removing standalone clip
from the upstream-first chain list. Update the terminal scheduler documentation
at lines 1758-1765 to include terminal clip alongside terminal group and dedup
as using downstream-first dispatch.

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