Add reference graphs for Crystal, Groovy, Prolog, and Tcl

[Widthdom]

Summary

• add conservative same-file reference graph extraction for Crystal, Groovy, Tcl, Prolog, and ambiguous .pl
• preserve ambiguous .pl classification while combining safe Perl and Prolog graph extraction
• surface and refresh dynamic graph-contract readiness across CLI, MCP, and status
• resolve Tcl namespace-qualified proc calls, preserve dict for state, and concatenate variadic after / namespace eval scripts
• mask Perl heredoc payloads before ambiguous .pl symbol and reference extraction
• precompute Prolog multiline-head parenthesis matches to keep malformed-input scanning linear under CI coverage
• keep capability-gap tests meaningful now that every built-in language advertises symbol/reference/graph support by using an explicit workspace search-only language fixture
• integrate the change with the latest origin/main, including the console-restoration stabilization from Stabilize console restoration assertions #4809

Validation

• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Release -f net8.0 --filter 'Issue4746|RunLanguages_|UnsupportedExtractorLanguage|EnsureConsoleWritersSynchronized|RunValidate_PositionalJson' — 120 passed
• equivalent .NET 9 focused run — 120 passed
• Issue Add reference graphs for Crystal, Groovy, Prolog, and Tcl #4746 / language-capability focused runs before the final main merge — 117 passed on both .NET 8 and .NET 9
• Prolog malformed multiline-head performance test with XPlat Code Coverage — passed; test body 472 ms
• broad .NET 8 remaining partition — 9,877 passed, 4 skipped; its sole console-restoration failure passed immediately in isolation and the subsequently fetched main included Stabilize console restoration assertions #4809's stabilization; the post-merge console-focused tests passed in both target frameworks
• dotnet build CodeIndex.sln -c Release --no-restore -p:UseSharedCompilation=false — 0 warnings, 0 errors
• focused dotnet format ... --verify-no-changes — clean
• dotnet run --project tools/CodeIndex.Changelog --no-restore -- check — 48 fragments valid
• cdidx status --check --json — workspace/index match; graph/index/fold complete; cap hits 0
• codex review --base origin/main — the issue-fix workflow's two review rounds were completed before this CI follow-up; all five actionable findings remain addressed

Documentation and changelog

• updated bilingual README, user, developer, testing, and status-contract guidance
• updated AGENT_GUIDE.md status-contract notes
• updated changelog.d/unreleased/4746.added.md

Follow-up candidates

• None.

Fixes #4746