chore: remove legacy CLI bootstrap and unused deps

Remove InitCliMode/RunCli, @CliFunction decorator, and
CliFunctionsRepository. The only registered CLI mode was `print-input`
which is unused — all real CLI functionality lives in the orchestrator
repo now.

This drops 3 dependencies:
- commander-ts (decorator-based CLI, needed reflect-metadata)
- reflect-metadata (peer dep of commander-ts)
- commander (only used for OptionValues type)

Cli.options, Cli.isCliMode, and Cli.query remain — the orchestrator
plugin sets these directly without commander.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

yarn.lock

@@ -2302,17 +2302,6 @@ __metadata:
   languageName: node
   linkType: hard
 
-"commander-ts@npm:^0.2.0":
-  version: 0.2.0
-  resolution: "commander-ts@npm:0.2.0"
-  dependencies:
-    commander: "npm:^7.2.0"
-  peerDependencies:
-    reflect-metadata: ^0.1.13
-  checksum: 10/b57582d0eb98e7bce0a05bfe7c44b8ed01a0f77a05358ec9d35ef6406ac6b3031590fa49e1bff58649ae511bb18a576b01151cb94de9c12c7f0be7f865ca494f
-  languageName: node
-  linkType: hard
-
 "commander@npm:^10.0.1":
   version: 10.0.1
   resolution: "commander@npm:10.0.1"
@@ -2341,13 +2330,6 @@ __metadata:
   languageName: node
   linkType: hard
 
-"commander@npm:^9.0.0":
-  version: 9.5.0
-  resolution: "commander@npm:9.5.0"
-  checksum: 10/41c49b3d0f94a1fbeb0463c85b13f15aa15a9e0b4d5e10a49c0a1d58d4489b549d62262b052ae0aa6cfda53299bee487bfe337825df15e342114dde543f82906
-  languageName: node
-  linkType: hard
-
 "common-path-prefix@npm:^3.0.0":
   version: 3.0.0
   resolution: "common-path-prefix@npm:3.0.0"
@@ -4214,13 +4196,6 @@ __metadata:
   languageName: node
   linkType: hard
 
-"reflect-metadata@npm:^0.1.13":
-  version: 0.1.14
-  resolution: "reflect-metadata@npm:0.1.14"
-  checksum: 10/fcab9c17ec3b9fea0e2f748c2129aceb57c24af6d8d13842b8a77c8c79dde727d7456ce293e76e8d7b267d1dbf93eea4c5b3c9101299a789a075824f2e40f1ee
-  languageName: node
-  linkType: hard
-
 "regexp-tree@npm:^0.1.27":
   version: 0.1.27
   resolution: "regexp-tree@npm:0.1.27"
@@ -4816,8 +4791,6 @@ __metadata:
     "@typescript/native-preview": "npm:^7.0.0-dev.20260505.1"
     "@vercel/ncc": "npm:^0.36.1"
     "@vitest/coverage-istanbul": "npm:^4.1.5"
-    commander: "npm:^9.0.0"
-    commander-ts: "npm:^0.2.0"
     cross-env: "npm:^7.0.3"
     eslint: "npm:^10.3.0"
     eslint-plugin-unicorn: "npm:^64.0.0"
@@ -4829,7 +4802,6 @@ __metadata:
     node-fetch: "npm:2"
     oxfmt: "npm:^0.48.0"
     oxlint: "npm:^1.63.0"
-    reflect-metadata: "npm:^0.1.13"
     semver: "npm:^7.5.2"
     ts-md5: "npm:^1.3.1"
     ts-node: "npm:10.8.1"