feat(sort): thread --sort-stats diagnostics through the chain

[nh13]

What

fgumi sort runs entirely on the declarative chain builder, but --sort-stats was inert on that path — it emitted warn!("--sort-stats is ignored by the sort chain (not yet threaded)") and produced no diagnostics. This threads the flag through so it actually works.

Change

• SortOptions gains a sort_stats: bool field, projected from the CLI flag by to_sort_options(), and wired into SortMerge::with_sort_stats(bool) in both the terminal and intermediate add_sort chain branches (the intermediate branch matters for a fused runall sort).
• The SortMerge merge-loop diagnostic (Sort merge diag: stalls=… contention=… output_full=…) is now gated behind --sort-stats. Previously it was logged unconditionally on every sort — the opposite bug — so this also makes an always-on diagnostic opt-in, matching the --sort-stats policy established in feat(sort)!: put the performance diagnostics behind --sort-stats #826.
• The single-source in-memory fast path (emit_fast_batches) now emits a short Sort fast-path diag: note under --sort-stats, so the flag is never a silent no-op even when the sort doesn't spill (no k-way merge to report).
• The stale warn! shim is deleted.

Behavior change to call out

• --sort-stats now produces output (was inert).
• The Sort merge diag: line no longer prints on every sort — it now requires --sort-stats. A run that previously showed it unconditionally will need the flag.

Scope note

This threads and gates the existing narrow SortMerge diagnostic; it does not restore the pre-cutover owned engine's richer (~100-line) per-phase diagnostics — that would be new instrumentation for a separate PR. The --sort-stats help text and the docs/src/guide/performance-tuning.md "Sort Statistics" section are rewritten to describe the current behavior accurately (one merge-diag line on spilling sorts; one fast-path note on in-memory sorts) and drop the now-false "own engine" claim.

Tests

• New tests/integration/test_sort_stats_diagnostics.rs: a spilling case asserts the merge diag is absent without --sort-stats and present with it (guarded by an assert_really_spilled check so it can't pass vacuously if memory accounting changes), plus a small-input fast-path case pinning that the fast-path note appears (and the merge diag does not).
• Updated the pre-existing test_sort_cutover_parity.rs assertion that had pinned the old always-on/ignored behavior, and its stale comments.

Full gate green: cargo ci-test 9956 passed / 31 skipped, plus ci-fmt/ci-lint/ci-doc and --no-default-features/--all-features.

Risk: sort diagnostics change command output, pinned by integration tests; unsafe changes: none, and CLAUDE.md allowlist updates: none; memory, queue, and thread/backpressure policy changes: none.

• Propagates --sort-stats through terminal and intermediate sort chains.
• Gates merge diagnostics behind the flag.
• Adds a diagnostic for single-source in-memory sorts.
• Removes the stale ignored-option warning.
• Updates documentation and integration tests for spilling and fast-path cases.

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• docs/src/guide/performance-tuning.md
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Walkthrough

--sort-stats is now active. The option reaches terminal and intermediate SortMerge steps. Diagnostics are emitted for spilling merges and in-memory fast-path execution when enabled.

Changes

Sort statistics diagnostics

Layer / File(s)	Summary
Conditional SortMerge diagnostics crates/fgumi-pipeline-io/src/sort/merge.rs	SortMerge stores a disabled-by-default sort_stats flag. with_sort_stats controls merge-loop and in-memory fast-path diagnostics.
Sort option pipeline wiring src/lib/commands/sort.rs, src/lib/pipeline/chains/builder.rs, src/lib/pipeline/chains/validate.rs, docs/src/guide/performance-tuning.md	sort_stats is added to SortOptions, propagated to terminal and intermediate sort steps, and documented as active.
Diagnostic and pipeline integration coverage tests/integration/main.rs, tests/integration/test_chain_bam_with_index.rs, tests/integration/test_sort_cutover_parity.rs, tests/integration/test_sort_stats_diagnostics.rs	Tests cover diagnostic gating, spilling and fast-path messages, removal of stale ignored-option warnings, and fused sort-to-group execution.

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

Merge Risk: ⚪ Minimal · up to 792ee

--sort-stats now enables diagnostics for spilling merges and single-chunk in-memory sorts without changing sorted output behavior. No current merge-blocking risk remains.

Sequence Diagram(s)

sequenceDiagram
  participant SortCommand
  participant SortOptions
  participant ChainBuilder
  participant SortMerge
  SortCommand->>SortOptions: copy sort_stats
  SortOptions->>ChainBuilder: provide sort_stats
  ChainBuilder->>SortMerge: call with_sort_stats
  SortMerge-->>SortCommand: emit merge or fast-path diagnostic

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Suggested labels: fgumi sort

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title follows the required Conventional Commit format and accurately describes threading --sort-stats diagnostics through the sort chain.
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

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.63%. Comparing base (247404b) to head (792eea5).
⚠️ Report is 4 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #913      +/-   ##
==========================================
+ Coverage   93.55%   93.63%   +0.07%     
==========================================
  Files         301      301              
  Lines      150626   150886     +260     
==========================================
+ Hits       140923   141281     +358     
+ Misses       9703     9605      -98     

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Actionable comments posted: 3

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Inline comments:
In `@src/lib/commands/sort.rs`:
- Line 437: Update the SortMerge documentation to reflect that FastPath requires
zero spill slots and exactly one in-memory chunk; no-spill execution with
multiple chunks still uses the merge path. In src/lib/commands/sort.rs lines
437-437, narrow the CLI help text to the single-chunk fast path; in
docs/src/guide/performance-tuning.md lines 296-296, distinguish no-spill
execution from FastPath execution.

In `@tests/integration/test_sort_stats_diagnostics.rs`:
- Around line 213-216: Strengthen the non-spilling sort-stats test by capturing
the chain logs and asserting that they contain FAST_PATH_DIAG_SUBSTRING when
sort_stats is enabled. Keep the existing sorted and grouped BAM assertions, and
target the test flow around sort_stats: true so it verifies propagation through
SortMerge::with_sort_stats rather than output alone.
- Around line 137-141: Extend the fast-path diagnostics tests around
sort_stats_on_fast_path_emits_fast_path_note_not_merge_diag with a case that
omits --sort-stats, then assert stderr does not contain FAST_PATH_DIAG_SUBSTRING
while preserving the existing enabled-case assertions.

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📥 Commits

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📒 Files selected for processing (9)

• crates/fgumi-pipeline-io/src/sort/merge.rs
• docs/src/guide/performance-tuning.md
• src/lib/commands/sort.rs
• src/lib/pipeline/chains/builder.rs
• src/lib/pipeline/chains/validate.rs
• tests/integration/main.rs
• tests/integration/test_chain_bam_with_index.rs
• tests/integration/test_sort_cutover_parity.rs
• tests/integration/test_sort_stats_diagnostics.rs

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