Add --workspace-root so file keys are repo-relative #219

Goal

Add an optional --workspace-root <dir> flag, with the same behavior as codeanalyzer-java (codellm-devkit/codeanalyzer-java#274). When it's set, file keys are relative to the workspace root instead of --input, so a project at packages/web/ in a monorepo produces packages/web/src/app.ts.

Design: docs/design/specs/2026-10-24-workspace-root.md in codeanalyzer-java (branch feat/add-workspace-root). Artifact and @external ids are language-neutral, so both analyzers must give the same repo-relative id for the same file.

Goals

• Add the --workspace-root option. Unset, the root is --input and output is byte-identical to today's.
• Use the root for symbol_table keys (discovery.ts), module ids and every id below them, and artifact keys/paths/ids (artifacts/index.ts).
• Keep the app segment as it is (--app-name, else the --input dir name). Artifact classification and on-disk reads stay relative to --input.
• Hard error if --input isn't inside the workspace root.
• Test that no key is absolute or contains ...

Definition of done

• Nested-fixture tests cover L1, L2 (call-graph ids) and L3 overlay ids.
• README documents the flag and that toggling it misses the cache.