Adds the design spec for PR-Q1 (post-cutover code quality sweep) and
finalizes the inbound-reference updates from the prior commit
(docs/CLI_MIGRATION.md links) that weren't staged at that point.

PR-Q1 is the first of three sequential sub-projects (quality -> speed
-> ID-rate +5% per dataset). Decomposed during the 2026-05-26
brainstorm because the three concerns differ in risk, scope, and time
profile; the ID-rate target is a multi-PR research project, not a
single ship gate.

Scope: 7 groups (6 in-PR + 1 out-of-repo memory update). Dangling
.java:LINE refs (42), stale "port of MS-GF+" framing, identifier
renames (MSGFRUST_RSS_PROBE etc.), 26 clippy warnings, lift CI lint
to required, remove shipped design specs.

The Java source tree was removed in commit b4565b8 during the
Rust-cutover; the inline citations to specific Java line numbers now
point at code that does not exist in this repo. Replace each citation
with intent-only "Java parity" comments. Preserves semantic meaning;
removes the broken hyperlinks.

Parity-test files (tests/*_java_parity.rs, tests/gf_bsa_parity.rs,
tests/*_match_java.rs) untouched — their identity is Java parity and
the citations are load-bearing documentation.

8 non-test files touched, 33 refs replaced, 0 functional changes.

The codebase is post-cutover; new contributors should read crate-lib
top-of-file doc comments as descriptions of what each crate does, not
as port-bookkeeping. CLI --help and enum doc comments that compared
behavior to Java's command-line options now describe behavior directly.

KEEPS user-facing provenance:
- README.md and DOCS.md project-lineage sections
- Legacy numeric flag values (Java MS-GF+ -X) in --help (user migration)
- (Java -precursorCal) in precursor_cal doc (exact flag name we mirror)
- docs/parity-analysis/** content
- Parity test files

Touched: 5 crate-lib headers + msgf-rust CLI framing.

The "MSGFRUST_" prefix dates from an early iter-era naming and does
not match the binary's identity (msgf-rust). Switch the primary name
to MSGF_RSS_PROBE and accept the legacy name for this release with a
one-line deprecation warning on stderr. The legacy name will be
removed in the next quality cleanup.

Side-effect-only env var; no functional change to search/scoring.

Brings the workspace to clippy-clean on stable 1.87.0 so the CI lint
job can be lifted from advisory to required in the next commit.

Changes by class:
- map_or simplifications: mechanical rewrite via clippy --fix
- complex-type aliases: SegmentPartitionCache, SegmentPartitionSlice,
  DeconvResult, and RankKeptCtx struct in
  crates/scoring/src/scoring/scored_spectrum.rs
- too_many_arguments: RankKeptCtx context struct in scored_spectrum.rs;
  #[allow] with reason for directional_node_score_inner, write_tsv,
  write_tsv_to, write_spectrum_rows, and compute_cleavage_credit
- doc-list indentation: add blank line after list / fix continuation
  indent at 15 sites in msgf-rust.rs and scored_spectrum.rs
- unused_mut, ? rewrite, manual split_once, loop-counter: via clippy --fix
- needless_range_loop: suppressed with reason (seg indexes cache AND
  serves as fallback partition_for arg)

No functional behavior change; PIN/TSV bit-identical regression gate
in tree (precursor_cal_bit_identical) is the verification.

After PR-Q1 Task 4 left the workspace clippy-clean on --lib targets,
remove continue-on-error from the lint job's clippy step and extend
the lint command to --all-targets (covers tests + examples + bin in
addition to lib).

Also addresses 5 residual warnings in test/example targets that the
--lib-only fix in Task 4 didn't reach:
- crates/scoring/examples/dump_main_ion.rs: struct field shorthand
- crates/scoring/examples/dump_prefix_cache.rs: needless_range_loop
- crates/scoring/tests/add_prob_dist_chunked_parity.rs: unnecessary parens

Rustfmt remains advisory (~11k lines of fmt churn pending; separate
cleanup).

Lint job now blocks PRs on clippy regressions.

Deletes the iter39 docs-rewrite spec and plan (shipped 2026-05-23 via
PR #30; the rewrite is in dev and being relied on, so the design docs
no longer need to be discoverable in the repo). Their lineage is in
git history.

Tracks the in-flight PR-Q1 implementation plan alongside its design
spec (committed in 55cff3f).

Future protocol: when a docs/specs design file references a feature
that has fully shipped and closed any deferred gate, remove it in the
next quality cleanup.

Three non-blocking observations from the final code review:

1. DOCS.md §97 documented only the legacy MSGFRUST_RSS_PROBE name.
   Now mentions MSGF_RSS_PROBE as the canonical with the legacy noted.
2. crates/model/src/amino_acid.rs:13 inline comment referenced the
   legacy name; updated to MSGF_RSS_PROBE.
3. log_rss deprecation warning fired on every call when only the
   legacy env var was set. Guard with std::sync::Once so it prints
   exactly once per process invocation.

All non-functional; verification: deprecation warning count is now 1
under MSGFRUST_RSS_PROBE=1 + multiple log_rss checkpoints.

After PR #35 (PR-Q1) closed unmerged for not delivering measurable
wins, pivot strategy: stack 3 loosely-coupled sub-features on top
of the cleanup commits and ship ONE PR with bench-gated value.

Sub-features:
- S1: profile-guided Astral wall reduction (gate: -5% wall)
- S2: LFQ calibrator threshold fallback 1e-6 -> 1e-5 (gate: +50 PSMs)
- S3: additive PrecursorErrorPpmSquared PIN column (gate: +50 PSMs
  on any one dataset)

Each sub-feature ships only if its bench gate passes; failures get
dropped before merge.

Profile (perf record on Astral cal=off, 285K samples) identified
36.82% of CPU in HashMap<Partition, ...> lookups using SipHash13.
The hot scoring path (compute_inner, directional_node_score_inner,
rank_scorer::error_score) repeatedly looks up Partition keys for
rank_dist_table, frag_off_table, ion_existence_table, etc.

Switch the 7 Param hot tables to FxHashMap (rustc-hash). SipHash13's
state-init + 13-round mix is unnecessary for non-cryptographic keys
on a single-process search; FxHasher is a single multiply-and-xor.
Same .get/.insert API; only iteration order differs (and no hot path
iterates these tables).

Expected: ~25-30% reduction in match_spectra wall on Astral cal=off.
Bench gate (S1) requires >= 5% Astral wall reduction to ship.

If the strict SpecEValue threshold (1e-6) does not qualify
MIN_CONFIDENT_PSMS (200) in the cal pre-pass, retry once at 1e-5
before giving up. Preserves Java parity on datasets where 1e-6 already
succeeds (Astral, TMT); recovers LFQ-shaped distributions where Rust's
SpecE-tail drift leaves the cal pre-pass a few PSMs short (LFQ ships
at 193/200 in PR-A).

Median-of-residuals + MAD-based robust sigma are robust to one decade
of noisier outliers; the fallback is a one-shot retry, not a baseline
threshold change.

Bench gate (S2): LFQ auto @1% FDR >= 14,805 (baseline 14,755 + 50).

This reverts commit 67002e4.

… tightening"

This reverts commit 9a6607a.

Re-profile on the PR-V1 binary (Astral cal=off, 245K samples) showed
the FxHashMap swap in scoring::Param did NOT close the dominant
hashing hotspot. 39.35% of CPU was still in the FnMut::call_mut
chain, which traces to:
  expand_mod_combinations -> AminoAcidSet::variants_for
  -> HashMap<(u8, ModLocation), Vec<AminoAcid>>::get
  -> hashbrown find_inner with std::hash::random::RandomState (SipHash13)

PR-V1 missed this map because it lives in the `model` crate, not
`scoring`. The candidate enumeration calls variants_for once per
peptide position per candidate; on Astral this dominates wall.

This commit:
- Adds rustc-hash as a model-crate dependency.
- Switches AminoAcidSet::table and aa_lists_cache from HashMap to
  FxHashMap. Same hashbrown internals; FxHasher is a multiply-and-xor
  vs SipHash13's 13-round mix.

No functional behavior change; PIN bit-identical regression gate
green. Tests pass.

Expected wall reduction on Astral cal=off: -10..-25%, depending on
how much of the 39% chain comes from the SipHash vs the surrounding
Arc clones and Vec extends.

…enum

A perf trace on the PR-V1 binary (Astral cal=off, 245K samples) showed
12.63%+ of CPU under `to_vec<AminoAcid>` and `Arc<Modification>::clone`
within the `expand_mod_combinations` -> `variants_for` chain. The
candidate enumerator was cloning the full Anywhere-variants Vec for
every interior position of every candidate peptide. For a length-L
peptide, L-2 of L positions had no terminal merging to do (typically
~87% of positions on real peptides) and the clone was pure waste.

Refactor: only the 1-2 terminal positions (pos 0 and pos L-1) build
owned merged variants via a new `build_terminal_variants` helper.
Interior positions reference the AminoAcidSet's Anywhere-variants slice
directly. `expand_recursive`'s signature changes from
`&[Vec<AminoAcid>]` to `&[&[AminoAcid]]`.

No functional behavior change; bit-identical regression gate green.

Expected wall reduction on Astral cal=off: -5..-15%, depending on
how much of the 12.63% chain is the `to_vec` vs the surrounding
recursion overhead.