feat: content-aware deduplication pre-pass in gradient transform

[BYK]

Summary

• Content-aware deduplication in the gradient transform pipeline: detects repeated tool outputs (same file read multiple times, identical command results) and replaces earlier occurrences with compact annotations, keeping only the latest.
• Two dedup levels: exact content hash (identical outputs) and same-file-path reads (different content from edits between reads).
• Runs as a pre-pass before layer selection (between layer 0 and layer 1), reducing token pressure so sessions can stay at lower, less lossy gradient layers.

Motivation

Inspired by Dirac's ContextManager approach: in long coding sessions, the same file is often read 2-5 times (explore → edit → verify). Each read stores the full content as tokens. A 500-line file appearing 3 times costs ~15K tokens; after dedup: ~5.1K. Those saved tokens can be the difference between layer 1 (clean window eviction, prompt caching preserved) and layer 2 (tool stripping, cache busted).

Design

• deduplicateToolOutputs(messages, currentTurnIdx) scans all completed tool parts, groups by content hash and file path, keeps the latest occurrence, replaces earlier ones with dedupAnnotation().
• Current turn is sacred — never touched.
• Tool parts are never removed — only state.output is replaced (preserves tool_use/tool_result pairing).
• Small outputs skipped — outputs below 600 chars aren't deduplicated (annotation would cost more than the original).
• Zero-cost no-op — returns original array reference when no duplicates exist.
• Follows existing toolStripAnnotation() pattern.

Files Changed

File	Change
src/gradient.ts	deduplicateToolOutputs(), dedupAnnotation(), simpleHash(), extractFilePath() + integration into transformInner()
test/gradient.test.ts	7 new tests: exact-match, same-file, current-turn protection, small-output skip, no-change passthrough, bash dedup, triple-read

Testing

• All 301 tests run, 298 pass, 3 fail (pre-existing vectorSearch test isolation issue from feat: multi-provider embeddings, distillation vector search, and cross-project recall #58, not introduced here)
• npx tsc --noEmit clean