fix(rust): resolve cargo clippy warnings and gate clippy in CI (#2096 follow-up)

[carlos-alm]

Problem

Follow-up to #2096: that issue's cargo fmt half landed (repo-wide reformat + cargo fmt --check CI gate). This PR does the cargo clippy half — as of #2096's investigation, cargo clippy reported ~98 warnings against crates/codegraph-core, and nothing in CI ran clippy.

What changed

Triaged 102 unique warning sites (as of this PR) across 21 lint categories:

• 17 categories, ~84 sites — mechanical, behavior-preserving fixes: unnecessary_map_or, double_ended_iterator_last, manual_contains, collapsible_match, doc_lazy_continuation, manual_pattern_char_comparison, collapsible_if, explicit_counter_loop, needless_lifetimes, needless_borrow, redundant_closure, redundant_pattern_matching, manual_flatten, needless_range_loop, nonminimal_bool, unnecessary_unwrap, manual_is_multiple_of.
• 3 categories, 7 sites — proper refactors: ptr_arg (narrowed &mut Vec<T> params to &mut [T] where the function never grows/shrinks the collection), new_without_default (added a Default impl delegating to the existing constructor), type_complexity (named type aliases for two-tuple-of-maps return types).
• 1 category, 11 sites — targeted #[allow] + deferred: too_many_arguments, all in the parity-critical call/edge-resolution hot path (dataflow.rs, pipeline.rs, build_edges.rs, import_edges.rs). A params-struct refactor here is exactly the kind of hasty structural change this issue's own body warns against; each site got a targeted (not blanket) #[allow(clippy::too_many_arguments)] with a justification comment. Refactor tracked in a follow-up: Closes... see below.

Added the CI gate: cargo clippy --workspace --all-targets -- -D warnings in the rust-check job, right after the existing cargo fmt -- --check step, mirroring how #2096 added that gate. Added clippy to the job's rust-toolchain components.

Follow-ups filed (out of scope for this PR)

• Params-struct refactor for too_many_arguments hot-path functions in codegraph-core (#2326 follow-up) #2481 — params-struct refactor for the 11 deferred too_many_arguments sites.
• bug(parity): jelly-micro bind.js/fun.js self-referential dynamic call edge missing on native engine #2482 — pre-existing (confirmed on a clean origin/main, unrelated to this change) dual-engine parity divergence: jelly-micro self-referential dynamic call edges.
• bug(parity): native engine emits far fewer dataflow vertices than WASM for JS/TS/pts-javascript fixtures #2483 — pre-existing (confirmed on a clean origin/main, unrelated to this change) dual-engine parity divergence: native engine emits far fewer dataflow vertices than WASM for several JS/TS/pts-javascript fixtures.

Test plan

• cargo clippy --workspace --all-targets -- -D warnings → 0 warnings
• cargo test --workspace → 1011 passed
• cargo fmt -- --check → clean
• Full JS/TS suite (npm test, native addon rebuilt fresh) → 5231 passed, 30 skipped, 2 todo, 0 failed
• npm run lint → clean
• Dual-engine parity tests (part of the full suite above) → passed
• node dist/cli.js diff-impact <merge-base> → no function-level impact (all touched files are under crates/**, outside codegraph's own JS/TS analysis scope, or the CI workflow file)

Closes #2326

[greptile-apps]

Greptile Summary

The PR clears existing Rust clippy warnings and makes clippy a required CI check.

• Adds clippy to the Rust CI toolchain and runs it across the workspace and all targets with warnings denied.
• Applies behavior-preserving lint simplifications across native extraction, analysis, graph building, persistence, and classification code.
• Introduces type aliases, slice-based parameters, Default support, and targeted justified lint allowances for deferred argument-structure refactors.

Confidence Score: 5/5

The PR appears safe to merge.

No blocking failure remains.

Important Files Changed

Filename	Overview
.github/workflows/ci.yml	Adds the clippy component and a workspace-wide all-targets clippy gate with warnings denied.
crates/codegraph-core/src/ast_analysis/dataflow.rs	Replaces explicit counters with enumeration, narrows mutable vector parameters to slices, and documents a targeted lint allowance.
crates/codegraph-core/src/db/connection.rs	Applies iterator and option idioms to database operations without changing reachable query-result behavior.
crates/codegraph-core/src/domain/graph/builder/pipeline.rs	Introduces return-type map aliases and a documented targeted allowance while preserving pipeline behavior.
crates/codegraph-core/src/domain/graph/builder/stages/build_edges.rs	Simplifies lifetimes, conditions, and option checks while retaining call-resolution and edge-emission behavior.
crates/codegraph-core/src/extractors/helpers.rs	Refactors string-node traversal into a guarded match arm while preserving long- and short-string handling.
crates/codegraph-core/src/extractors/javascript.rs	Applies equivalent pattern-matching, character-trimming, and condition simplifications to JavaScript extraction.
crates/codegraph-core/src/features/structure.rs	Applies clippy-oriented iterator and conditional simplifications to structure analysis.

_{Reviews (2): Last reviewed commit: "fix(rust): remove redundant borrow flagg..." | Re-trigger Greptile}