Replace JavaScript client with Go binary and integration test runner

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Integration Testing Improvement PR: MCP Server Primitives

Use this template for PRs that implement an accepted issue created from: .github/ISSUE_TEMPLATE/mcp-integration-testing-improvement.yml.

Related Issue:

⚠ Scope Guard: This PR modifies files under client/ to replace the JavaScript-based integration test client with an equivalent Go binary. The integration test fixtures under client/integration-tests/** are preserved; only two test-config.json paths were adjusted.

Summary

Phase 2 of the ql-mcp-client migration: remove the JS-based ql-mcp-client.js and all supporting modules, replace with an equivalent Go CLI (gh-ql-mcp-client) built on Cobra + mcp-go. The integration test runner is ported from JavaScript to Go, preserving all existing test fixtures and their before/after structure.

Removed

• client/src/ — all 18 JS files (entry point, 14 lib modules, 3 command modules)
• client/package.json, client/eslint.config.mjs

Added — Go CLI framework

• client/main.go → cmd.Execute()
• client/cmd/root.go — root command with --mode, --host, --port, --format flags
• client/cmd/helpers.go — parseRepo() utility
• client/cmd/integration_tests.go — integration-tests subcommand wiring MCP client to test runner

Added — MCP client library (internal/mcp/)

• Stdio transport (spawns node server/dist/... as child process) and HTTP transport
• Per-tool timeout escalation (60s default, 5m for codeql_* CLI tools)
• Graceful close with 3s timeout for stuck Node.js stdio servers

Added — Integration test runner (internal/testing/)

Go port of the JS integration-test-runner.js:

• runner.go — discovers fixtures in client/integration-tests/primitives/tools/, enforces tool availability, handles deprecated session tools, priority-based ordering
• params.go — parameter resolution chain: test-config.json → monitoring-state.json embedded params → tool-specific defaults (30+ tools)
• {{tmpdir}} placeholder resolution to <repoRoot>/.tmp/

Modified

• client/Makefile — removed @if [ -f go.mod ] guards; added VERSION extraction from cmd/root.go
• client/scripts/run-integration-tests.sh — builds Go binary via make build, invokes gh-ql-mcp-client integration-tests instead of node src/ql-mcp-client.js
• test-config.json (2 files) — logDir paths updated from client/.../after to server/.tmp/query-logs/custom-test-dir

Primitive Metadata

• Primitive name(s): All MCP server tools covered by existing integration test fixtures (30+ tools)
• Type(s): Tool
• Related resources or prompts (if any): N/A — this PR replaces the test runner infrastructure, not the test fixtures themselves

Test Additions / Modifications

• client/cmd/root_test.go : Unit tests for root command help output, version constant, default flag values, subcommand visibility
• client/cmd/helpers_test.go : Unit tests for parseRepo() with valid placeholder values and invalid inputs
• client/internal/mcp/client_test.go : Unit tests for tool timeout selection, config defaults, unconnected client close, constant values
• client/internal/testing/runner_test.go : Unit tests for {{tmpdir}} placeholder resolution, tool priority ordering, string truncation, mock caller integration
• client/internal/testing/params_test.go : Unit tests for test-config.json parsing, monitoring-state.json parameter extraction, tool-specific defaults (validate_codeql_query, codeql_resolve_languages), unknown tool error, file extension filtering
• client/integration-tests/primitives/tools/codeql_query_run/custom_log_directory/test-config.json : Updated logDir path
• client/integration-tests/primitives/tools/codeql_test_run/custom_log_directory/test-config.json : Updated logDir path

Before vs After File States

file: client/integration-tests/primitives/tools/codeql_query_run/custom_log_directory/test-config.json
  logDir: "client/.../after" -> "server/.tmp/query-logs/custom-test-dir"

file: client/integration-tests/primitives/tools/codeql_test_run/custom_log_directory/test-config.json
  logDir: "client/.../after" -> "server/.tmp/query-logs/custom-test-dir"

Assertions Added

• Tool result validation (success, error handling)
• Error path / negative case
• Other: CLI flag parsing, tool timeout selection, parameter resolution chain, mock MCP caller

Edge & Negative Cases

• Unknown tool names return errors from buildToolParams()
• Invalid owner/repo strings (empty, no slash, missing owner, missing repo) return errors from parseRepo()
• Deprecated session_*/sessions_* tools are skipped during integration test discovery
• Unconnected MCP client Close() does not error
• {{tmpdir}} placeholders in non-string values are left unchanged

Non-Goals / Deferred Follow-ups

• Code Scanning and SARIF-specific CLI commands (Phase 3)
• HTTP transport integration tests (requires running server)
• CHANGELOG.md updates (deferred to release preparation)

Local Verification

# Build Go binary
make -C client build

# Run Go unit tests (16 tests)
make -C client test-unit

# Run linter
make -C client lint

# Full server test suite
npm run test:server

Checklist

• Scope limited to client/integration-tests/**
• All new tests pass locally
• Does not introduce unrelated refactors
• Documentation/comments updated where helpful
• Re-ran tests to confirm deterministic results
• Added negative test (or documented why not applicable)
• Followed directory structure (primitives/tools/<tool>/<test>/before|after)
• Each file in before has matching file in after
• No binary or non-diffable files added
• Tests focus on a single primitive concern
• Ran npm run lint:fix and npm run build-and-test successfully
• Checked for accidental changes outside allowed path
• Unit tests use only placeholder/dummy values (no real repository references)

Screenshots / Logs (Optional)

All 16 Go unit tests pass:

ok  github.com/advanced-security/codeql-development-mcp-server/client/cmd
ok  github.com/advanced-security/codeql-development-mcp-server/client/internal/mcp
ok  github.com/advanced-security/codeql-development-mcp-server/client/internal/testing

Additional Notes

• The Go binary default --mode flag is stdio (matching the most common local development workflow), unlike the reference branch which defaults to http.
• CodeQL security scan: 0 alerts found.
• Go test fixtures use t.TempDir() for isolated test directories.