fix: recover truncated ingest output and cap clip retries

[AndrewDongminYoo]

Summary

• Retry incomplete FILE blocks once with a targeted, bounded generation request.
• Allow only the originally truncated paths in repair output and avoid caching unrecovered partial output.
• Enforce the clip server restart limit instead of resetting the counter after every successful bind.

Root cause

• Provider streams can end mid-FILE; the parser dropped the incomplete block with a warning but did not attempt targeted recovery. CLI transports also cannot apply the configured max_tokens override.
• The clip server reset restart_count immediately after every bind, so repeated server-loop exits could never reach MAX_RESTART_RETRIES.

Verification

• npm run test:mocks — 118 files, 1,722 tests passed
• npm run typecheck
• npm run build
• npm --prefix mcp-server run build
• cargo fmt --manifest-path src-tauri/Cargo.toml -- --check
• cargo test --manifest-path src-tauri/Cargo.toml --lib — 348 passed, 1 ignored
• cargo check --manifest-path src-tauri/Cargo.toml --message-format=short
• git diff --check upstream/main...HEAD