chore(deps): bump @molcrafts/molrs to 0.0.14 + io/overlay/runtime cleanup

[Roy-Kid]

Summary

• Bumps @molcrafts/molrs from ^0.0.12 to ^0.0.14. The only breaking
  change in 0.0.13 is the LAMMPSDumpReader rename to LAMMPSTrajReader;
  this PR adopts the new name in core/src/io/reader.ts and
  core/tests/test_wasm.ts.
• Bundles the in-flight refactors that grew alongside the bump so master
  lands in one coherent state instead of two interleaved series.

Changes by area

@molcrafts/molvis-core

• io: replace normalize_coords with a column-based atom_coords
  helper plus a lazy frame reader (lazy_reader.test.ts,
  data_source_modifier.test.ts).
• overlays: revamp the mark_atom overlay flow (composite mark + new
  types).
• commands: refactor commands/index, frame, mark_atom, and
  place_molecule around the updated entity_source / scene_index
  plumbing.
• rpc: move buildFrame / buildBox tests from page/ to
  core/tests/serialization.test.ts, where the helpers actually live
  since b5dca14 (recovers coverage that was orphaned at that move).
• Misc trajectory / scene-index / modifier / pipeline cleanup.

vsc-ext

• Split pathUtils.ts into pure helpers (type-only vscode import) and
  a new activeUri.ts that owns the runtime vscode.window dependency.
  This lets pathUtils unit tests load outside the extension host.
• Tighten tsconfig.test.json include glob so it only pulls in files
  the unit tests actually exercise — fixes the rootDir violation
  triggered by @molvis/core/io/formats resolving to core/src/io/.
• Rename rslib.{extension,webview}.config.ts → .mts for proper ESM
  resolution.

page

• Drop the orphaned test_wasm_serialization.ts (the helpers moved to
  core in b5dca14). Add --passWithNoTests so an empty page test suite
  exits cleanly.

molvis (Python)

• New molvis.runtime module + tests.
• scene / commands/overlay / commands/catalog updates wired
  through to the new runtime.
• Drop the install_widget_stubs leftover from test_control /
  test_video (the modules they import no longer require it).

Tooling

• biome.json: ignore .venv, .rslib, out, out-test so a fresh
  checkout matches the CI environment.
• Format package.json per Biome's expectation (workspaces array
  inline).

Test plan

• npx biome check — 0 errors, 14 warnings (all configured warn)
• npm run typecheck — core + page + vsc-ext all green
• npm run test:core — 382 / 382 passed
• npm run test:vsc-ext — 6 / 6 passed (mocha unit tests now load
  the split pathUtils without vscode runtime)
• npm run test:python — 98 passed, 2 skipped (PIL / ffmpeg
  optional)
• npm run build:all — core dist + page bundle (→
  python/src/molvis/dist/) + vsc-ext extension & webview all
  green; molrs_bg.wasm bundled at the new 0.0.14 SHA.

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