fix: preserve CodeDiff version alternatives

[jlitola]

Outcome

• Preserve PkgSeer CodeDiff available_versions in backend order through the bounded core parser and shared CLI/MCP error envelope.
• Keep each package version paired with its proven source ref; render ref-only alternatives as refs rather than package versions.
• Retain arbitrary-extension filtering and existing success, error, ref-suggestion, ranking, and retry behavior.
• Document the CodeDiff-specific availableVersions semantics and add patch release impact for both githits and @githits/mcp.

Verification

• bun test packages/core-internal/src/services/code-navigation-service.test.ts packages/mcp/src/shared/code-navigation-error-map.test.ts src/tools/code-diff-parity.test.ts src/commands/code/diff.test.ts — 145 passed, 0 failed.
• bun run typecheck and targeted Biome lint/format — passed.
• Root and @githits/mcp builds — passed.
• bun run validate:packages — passed.
• Source and built CLI/MCP smoke suites — passed.
• Exact rebuilt dev CLI JSON returned ten ordered details.availableVersions entries for npm:express 3.21.2..4.15.5; text rendered explicit version/ref pairs with the existing bounded list.

Review

• Internal code review: clean.
• Fresh Claude Opus review: one documentation scope correction fixed in b2f1080; follow-up round clean.

Known validation note

The exact direct bun run dev invocation stayed idle and was stopped. Authenticated source smoke exercised CodeDiff successfully, and the exact rebuilt Node artifact validated the failing dev error path in JSON and text.