fix(mcp): distinguish untracked resource diagnostics

[vcheckk]

Closes #132.

What changed

• Changes resource reads so clients can distinguish untracked files from tracked clean files.

Validation

• Included in standalone integration branch restart-standalone-integration.
• cargo test -p mcpls-core passed.
• cargo clippy -p mcpls-core --all-targets -- -D warnings passed.
• Real rust-analyzer smoke passed: cargo test -p mcpls-core --test integration_tests integration::rust_analyzer_tests::test_hover_on_u64_type -- --ignored --exact --nocapture.

[bug-ops]

Closing this PR as part of a batch closure of all submissions from this contributor.

The entire set of 15 PRs (#180–#194) was submitted within ~3 minutes on 2026-06-13, indicating AI-generated code submitted without proper individual review or integration into the project's contribution workflow.

Specific issues identified across the batch:

• PRs opened against issues explicitly marked as blocked (e.g. fix(bridge): split notification cache lock #180 closes fix(bridge): split NotificationCache out of Translator lock to eliminate notification_pump starvation #104 which is blocked by Document tracker never re-reads files after first didOpen — every external edit yields stale results #102)
• Nested mutex anti-patterns introduced (perf(bridge): remove translator mutex from tool requests #181: Mutex inside Mutex)
• Incomplete refactors (read_resource contention path not updated in fix(bridge): split notification cache lock #180)
• Breaking API changes without coordination (feat(config): route tools to named LSP servers #194 changes registration key from language_id to server_key)
• Stacked PRs submitted as independent PRs without proper base branch setup

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