Fix -y short flag collision between --yaml and --yes (#559)

[CodersAcademy006]

Summary

In RunContext.cli_command (nemo_run/cli/api.py), both --yaml and --yes/--no-confirm claimed the short flag -y, so Click emitted a warning on every invocation. This drops -y from --yaml and keeps it as the conventional alias for --yes.

Closes #559

cc @hemildesai @marcromeyn

[CodersAcademy006]

@ko3n1g @chtruong814 could one of you take a look at this and at #562? Both have been open since July 14 with no reviewer assigned, and the original cc to @hemildesai and @marcromeyn was not picked up.

This one is a single line in nemo_run/cli/api.py. In RunContext.cli_command both --yaml and --yes/--no-confirm claim the short flag -y, so Click emits a warning on every invocation. It drops -y from --yaml and leaves it as the conventional alias for --yes. Closes #559.

[svcnemo-autobot]

PR #561 — needs attention
Blocking findings: None.
Non-blocking finding: docs/guides/cli.md:349 still advertises -y for --yaml, while nemo_run/cli/api.py:893-900 now reserves -y for --yes. Update the generated/example option table so users are not given a removed alias.
Validation gaps: No regression test asserts warning-free help or verifies that -y selects confirmation bypass. Only DCO is visible.

[ko3n1g]

@CodersAcademy006 could you take a look at #561 (comment) please?

[CodersAcademy006]

Hey @ko3n1g Fixed all three blockers. Removed -y from yaml option in api.py line 894, updated docs at 349, added TestShortFlagCollision regression tests to verify -y works for skip_confirmation and yaml has no short flag. Ready to merge.