Add optional agent guidance baseline to basectl repo

[codeforester]

Problem

Base already helps managed repositories standardize baseline project shape and GitHub workflow, but basectl repo cannot currently seed or check repo-local agent workflow guidance.

That leaves each repo to hand-author the same durable files when it wants AI-assisted contribution rules:

• AGENTS.md
• skills.md
• .github/pull_request_template.md
• related validation/docs hooks

Base and Banyan Labs now both benefit from this pattern, but existing repositories need a safe, opt-in path. Base should not silently overwrite repo-specific guidance or manage personal Codex runtime settings.

Desired Outcome

Add an optional basectl repo capability that can seed and validate a repo-local agent guidance baseline for Base-managed repositories.

Scope

• Design the command shape for opt-in agent guidance support, such as a flag on existing basectl repo commands or a focused subcommand.
• Provide templates for repo-local guidance files:
  • AGENTS.md
  • skills.md
  • .github/pull_request_template.md
• Support dry-run behavior that reports planned creations or checks before writing.
• Leave existing files unchanged unless the user explicitly requests an update path.
• Include placeholders or generated values for repository name, default branch, worktree path convention, labels, and validation commands.
• Allow basectl repo check to report missing agent guidance only when the repo has opted into the baseline.
• Update Base documentation for the new repo baseline behavior.
• Add focused tests for generation, dry-run/check behavior, and existing-file preservation.

Non-Goals

• Do not install the Superpowers plugin.
• Do not manage ~/.codex/config.toml, personal Codex skills, or user-local runtime settings.
• Do not vendor third-party agent methodology files directly.
• Do not move project-specific service or product behavior into Base.
• Do not overwrite existing repo-local guidance without an explicit update workflow.

Acceptance Criteria

• The command design is documented before implementation.
• A new or existing basectl repo command can create the guidance baseline in an empty or test repository.
• Dry-run output names the guidance files that would be created.
• Existing guidance files are preserved by default.
• Opted-in repo checks can report missing guidance files with actionable output.
• Docs explain the boundary between Base-owned repo baseline support and repo-owned agent guidance content.
• Tests cover the baseline generation/check behavior.

Validation

• Relevant basectl repo tests.
• git diff --check.
• env -u BASE_HOME ./bin/base-test if the change touches shared Base behavior.

Demo Impact

Likely useful for a short basectl repo demo once implemented, because it shows Base helping managed repos adopt durable agent workflow guidance without taking over project-specific rules.