refactor: reorganize src/ from flat files into deep modules

[mfaux]

Summary

Reorganizes src/ from a flat ~97-file structure into deep modules by feature. Each cluster of related files moves into its own directory with a barrel index.ts that re-exports only the public API. Shared code moves into src/lib/ organized by domain. Command modules each get their own directory.

Closes #28

Changes

• src/lib/git/ — git.ts, gitignore.ts, github-trees.ts + tests
• src/lib/lock/ — dotai-lock.ts, skill-lock.ts, local-lock.ts, lock-version-error.ts + tests
• src/lib/parsers/ — source, prompt, agent, instruction, override parsers + tests
• src/lib/transpilers/ — prompt, agent, instruction transpilers + tests
• src/lib/discovery/ — context, skill, find discovery + tests
• src/lib/install/ — context installer/add/check, skill installer, collisions, append markers + tests
• src/lib/agents/ — agents.ts, target-agents.ts
• src/lib/ — types.ts, utils.ts, constants.ts, validation.ts, model-aliases.ts, telemetry.ts, plugin-manifest.ts, command-result.ts, test-utils.ts, prompts/, providers/
• src/add/ — add command and all sub-modules + tests
• src/check/, src/find/, src/init/, src/list/, src/remove/, src/restore/, src/sync/ — each command in its own directory with barrel index
• Normalized ~14 import statements from .js to .ts extensions
• Updated all imports in tests/ directory for new module locations

Approach

• Pure structural refactor: file moves and import updates only. No logic changes, no behavior changes.
• Each commit is self-contained: move files, create barrel, update all imports.
• pnpm build, pnpm test, pnpm type-check, and pnpm format:check all pass.

Resulting structure

src/
  cli.ts, cli-parse.ts          # entry point + arg parsing
  add/                           # add command
  check/ find/ init/ list/       # other commands
  remove/ restore/ sync/
  lib/
    agents/ discovery/ git/      # shared modules by domain
    install/ lock/ parsers/
    transpilers/ prompts/
    providers/
    types.ts utils.ts constants.ts ...