test(integration): add real-repo SCIP integration tests for all supported languages

[jafreck]

Summary

Adds deterministic integration tests that clone real open-source repos, build them, index via SCIP, and query MCP tool handlers — validating the full pipeline for every SCIP-supported language.

What's included

Integration test framework (tests/integration/)

• harness.ts — shared helpers: prepareRepo (clone → build → index → open DB), tool handler wrappers (lookupSymbol, queryCallees, searchSymbols, findDependents, analyzeStructure, getSnippet, etc.), BuildCommand support, getIndexStats
• zod.test.ts — TypeScript (18 tests)
• fastapi.test.ts — Python (21 tests)
• lore-self.test.ts — TypeScript/Lore (19 tests)
• scip-languages.test.ts — parametric tests for 10 additional languages (110 tests):

Language	Repo	Indexer	Build step
Java	jackson-databind	scip-java	./mvnw compile
Go	gin	scip-go	—
Rust	once_cell	rust-analyzer	cargo check
C	cJSON	scip-clang	cmake auto-compdb
C++	nlohmann-json	scip-clang	cmake auto-compdb
C#	Humanizer (v2.14.1)	scip-dotnet	dotnet build
Ruby	jekyll	scip-ruby	—
PHP	PHPMailer	scip-php	composer update
Kotlin	moshi	scip-java	— (scip-java wraps Gradle)
Scala	playframework	scip-java	— (scip-java wraps sbt)

SCIP pipeline bug fixes

Found and fixed 5 bugs via the integration tests:

1. scip-ruby registry — was ['--output', '{output}'], scip-ruby uses bare ['.'] and writes index.scip
2. scip-php registry — was ['index', '--output', '{output}'], scip-php runs bare [] and writes index.scip
3. scip-dotnet {project} discovery — was index . which requires a root .sln; added {project} placeholder with auto-discovery of .sln/.csproj files up to one directory deep
4. Non-zero exit code recovery — loadScipIndexes now checks for index.scip output when the indexer exits non-zero (e.g., scip-ruby exits 100 with warnings but writes valid output)
5. C# language detection — detectProjectLanguages now finds .sln/.csproj files by extension in the directory scan, not just by exact filename match at root

CI workflow (.github/workflows/integration.yml)

Runs integration tests on push to main and weekly schedule, with all SCIP indexers installed.

Config changes

• .gitignore — added .integration-repos/
• vitest.config.ts — excluded .integration-repos/ from test discovery and tests/integration/harness.ts from coverage

Test results

All tests gated behind INTEGRATION=1. Without it, all 168 tests skip cleanly.

With INTEGRATION=1: 163/168 pass. The 5 remaining failures are external tool limitations:

• PHP scip-php doesn't emit call refs (only definitions)
• Kotlin scip-java needs JDK 17 for moshi's records-tests subproject toolchain
• Scala scip-java needs >120s for full sbt compile from clean checkout (timeout)

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.31%. Comparing base (ad2d825) to head (d2af68f).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #468      +/-   ##
==========================================
+ Coverage   91.83%   92.31%   +0.47%     
==========================================
  Files          65       65              
  Lines        6160     6193      +33     
  Branches     1715     1723       +8     
==========================================
+ Hits         5657     5717      +60     
+ Misses        503      476      -27     

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