[Audit] Normalize CLI option naming: --agent vs --agents inconsistency

[rohitg00]

Problem

CLI option naming is inconsistent across commands:

Command	Flag	Type
install	--agent	Array
install	--skills,--skill,-s	String (comma-separated)
generate	--agents	(plural)
manifest	--agents	(plural)
translate	--to	(different pattern entirely)

Users must remember different flag names per command.

Proposed Solution

Standardize on:

• --agent (singular, Array type) — consistent with install command
• --skill (singular, with -s shorthand) — filter by skill name
• Accept both --agent and --agents as aliases for backwards compatibility
• Deprecation warning for --agents: "Use --agent instead (--agents will be removed in v2.0)"

Files to Update

• packages/cli/src/commands/generate.ts — --agents → --agent
• packages/cli/src/commands/manifest.ts — --agents → --agent
• Any other commands using plural form

Acceptance Criteria

• All commands use --agent (singular) as primary flag
• --agents accepted as deprecated alias
• Deprecation warning shown when --agents is used