fix(cli): deprecate explicit command support for agy (#1798) (#1808)

* fix(cli): deprecate explicit command support for agy (#1798)

* docs(cli): add tests and docs for agy deprecation (#1798)

* fix: address review comments for agy deprecation

* fix: address round 2 review comments for agy deprecation

* fix: address round 3 review comments for agy deprecation

* fix: address round 4 review comments for agy deprecation

* fix: address round 5 review comments for agy deprecation

* docs: add inline contextual comments to explain agy deprecation

* docs: clarify historical context in agy deprecation docstring

* fix: correct skills path in deprecation comment and make test mock fully deterministic