refactor: group src/lib and src/commands into domain folders

[vreshch]

Mechanical directory restructure: git mv + import-path updates only. No logic changes, no renames, no new exports, no barrels.

What changed

src/lib/ and src/commands/ files grouped into domain subfolders. Each source file moved with its co-located *.test.ts via git mv (history preserved).

Before

src/lib/          http.ts origins.ts config.ts file-lock.ts oauth.ts callback-server.ts
                  api.ts provision.ts vaults.ts vaults.schema.ts vault-registry.ts
                  daemon-client.ts daemon-pref.ts memory-client.ts status-info.ts
                  update-check.ts update-cache.ts update-lock.ts
src/commands/     setup.ts status.ts vault.ts vault-sync.ts memory.ts memory-verbs.ts
                  daemon-cmd.ts mcp.ts update.ts

After

src/lib/net/      http.ts origins.ts
src/lib/fs/       config.ts file-lock.ts
src/lib/auth/     oauth.ts callback-server.ts api.ts provision.ts
src/lib/vault/    vaults.ts vaults.schema.ts vault-registry.ts
src/lib/daemon/   daemon-client.ts daemon-pref.ts
src/lib/memory/   memory-client.ts
src/lib/status/   status-info.ts
src/lib/update/   update-check.ts update-cache.ts update-lock.ts

src/commands/auth/     setup.ts
src/commands/status/   status.ts
src/commands/vault/    vault.ts vault-sync.ts
src/commands/memory/   memory.ts memory-verbs.ts
src/commands/daemon/   daemon-cmd.ts
src/commands/mcp/      mcp.ts
src/commands/update/   update.ts

Import updates

• All relative .js ESM imports re-resolved for moved files and their consumers across src/commands, src/daemon, src/sync/{couch,git,discover}, src/mcp, src/daemon-entry.ts, src/cli.ts.
• Fixed stale vi.mock(...) path strings in daemon-cmd.test.ts, mcp.test.ts, status-info.test.ts, update-check.test.ts (string literals that must match their import specifiers).
• Adjusted the update-lock.test.ts transpile fixture to mirror the new fs/ + update/ subfolder layout (it copies sibling sources by name; assertions unchanged).
• No index/barrel files added. No files renamed. No exports/logic changed.

Docs

• Updated CLAUDE.md Layout section to reflect the new subfolders.
• README has no file-tree section; architecture diagram untouched.

Verify

• npm run verify fully green: type-check + type-check:e2e + lint + format:check + 406 unit tests + build.
• Sanity-ran the built CLI: node dist/cli.js --help and node dist/cli.js status resolve modules and run without crashing.

Files moved: 53 (with tests). Import/mock lines changed: 125.

[github-actions]

🎉 PR Validation ✅ PASSED

Commit: b2473dfba291a4cd15e047281360a05982a494e3
Branch: feature/structure-domain-folders

Checks:

• ✅ Release guard (no version/changelog changes)
• ✅ Dependencies installed
• ✅ Type check passed
• ✅ Linting passed
• ✅ Format check passed
• ✅ Tests + coverage passed
• ✅ Build successful

Ready to merge! ✨

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⏰ Generated at: 2026-07-08T21:40:43.509Z