Plan deprecation of `agentseek api` passthrough commands

[PsiACE]

Summary

Plan the deprecation of the agentseek api passthrough command group so the top-level AgentSeek CLI can focus on a unified project lifecycle.

Design Questions

• Should agentseek api be deprecated before removal, or removed directly before the next stable release?
• What migration path should users follow for agentseek-api workflows?
• Which docs, examples, templates, and tests currently reference agentseek api?
• How should the CLI communicate the deprecation during the transition?
• Should agentseek-api remain a separate package with its own CLI entry point?

Expected Outcome

• A deprecation and migration plan for agentseek api.
• A list of affected docs, examples, templates, and tests.
• Follow-up issues for implementation, documentation updates, and eventual removal.