refactor: domain error hierarchy (ROADMAP 3.8)

[carlos-alm]

Summary

• Add src/errors.js with structured domain error hierarchy: CodegraphError base class + 7 subclasses (ParseError, DbError, ConfigError, ResolutionError, EngineError, AnalysisError, BoundaryError)
• Replace all process.exit(1) calls in library code (embedder, db/connection, watcher, mcp/server, snapshot) with thrown domain errors
• Replace all throw new Error() in library code (ast-analysis/shared, batch, db/query-builder, db/repository/nodes, native, snapshot) with appropriate domain error subclasses
• CLI top-level catch formats CodegraphError with [CODE]: message prefix; MCP catch returns structured { isError, code } responses
• CI gate commands (check, manifesto) use process.exitCode = 1 instead of process.exit(1)
• CLI uses parseAsync() so async command errors propagate to the top-level handler
• All error classes exported from the public API (src/index.js)

Test plan

• New tests/unit/errors.test.js — 16 tests covering all classes, instanceof chain, option forwarding
• Updated tests/unit/db.test.js — asserts DbError instead of process.exit spy
• Updated tests/unit/prompt-install.test.js — asserts EngineError instead of process.exit spy
• All existing tests pass (97/97 in affected files)
• Lint clean (biome check passes)
• Zero process.exit(1) remaining in library code (only in CLI entry point)
• Zero throw new Error remaining in src/