Refactor: deepen internal modules and table-driven flag parsing

[renezander030]

Internal refactor with no behaviour change. Duplicated logic moves behind small internal modules, and the CLI flag parser becomes table-driven.

Changes

• Atomic writes: a new src/atomic-write.ts holds the temp + fsync + rename staging. The user-enums catalogue and the app-version tracker now use the same random-name, exclusive-create temp file as draft saves. draft.writeAtomic keeps its signature.
• JSON metadata reads: readJsonObjectFile / parseJsonObject (in bom.ts) replace seven hand-rolled read-and-parse copies in register, rename, media registration and the CLI. An absent file and a corrupt one remain distinct outcomes.
• register / rename: one guard now handles the "changed on disk after it was planned" refusal for both commands.
• Segment lookup: requireSegment (src/segment-lookup.ts) replaces 17 find-or-throw copies and saveTemplate's own search loop. The error message is unchanged.
• detect-scenes / detect-silence: both run their ffmpeg pass through runFfmpegAnalysis (src/ffmpeg-pass.ts). Each keeps its own error labels and hints.
• Flag parsing: 165 single-field flags (boolean, text, float, integer, Number) move from parseFlags branches into typed tables. A table entry that doesn't match its Flags field fails type-checking. Flags with validation, multiple values or command scoping keep their branches.
• Dead code: removes the unused detectStoreAppVersion and mattingState.

src/ goes from 23,330 to 23,119 code lines, not counting blanks and comments.

Verification

• npm run build, npm test (1228 tests, 0 failures; 10 new), npm run lint, npm run wasm:verify, Python client unit tests, npm pack + npm run smoke:package, all on Node 20.
• New tests pin current behaviour, and each passes on master as well as on this branch:
  • the changed-on-disk refusal and --force-write for rename and register
  • exact ffmpeg failure messages for both detectors (unavailable, timeout, buffer overflow, non-zero exit)
  • absent / BOM / non-object JSON reads
  • atomic state-file writes
• Old and new parseFlags return identical results on 107,996 argument vectors: every flag, in every command context, with the value present, missing, flag-like and repeated.
• Public surface is unchanged:
  • --help and every <command> --help
  • describe output
  • lib.js exports
  • all shipped .d.ts files (byte-identical)

Review notes

• Base: bc7d4c3. One commit per change, so the PR can be reviewed commit by commit.
• No stored formats, config paths, command registrations or shipped type declarations change.
• Merges cleanly with translate: default to Claude Haiku 5.5 #143 and Fix: portable skill scripts + two read-path bugs found on a JianYing 9.0.0 host #149, which also touch src/index.ts / src/caption.ts.
• CI covers the Node 18/22, macOS and Windows matrix entries that were not run locally.