feat: configure code-mode agent file policy

[upu (upu)]

Summary

• add a committed openwiki.config.yaml setting at codeMode.agentFiles.policy with manage and preserve values
• keep manage as the backward-compatible default and resolve policy in the order CLI > config > default
• add --agent-files-policy <manage|preserve> as a one-run code-mode override
• make preserve leave existing root AGENTS.md and CLAUDE.md byte-for-byte unchanged and keep missing files absent
• make newly generated scheduled workflows read the committed config, omitting agent files from add-paths when the committed policy is preserve
• cover precedence, init/update/chat paths, workflow behavior, invalid config, CLI parsing, and help output
• document the configuration and include a minor changeset

Configuration

codeMode:
  agentFiles:
    policy: preserve

The agentFiles mapping keeps policy separate from possible future path configuration. A CLI override applies only to the current run and never rewrites or creates the config file.

Why

Some repositories already have an intentional agent-instruction layout. For example, a repository may keep shared guidance in /AGENTS.md and use /.claude/CLAUDE.md only as a pointer to it, with no root /CLAUDE.md by design.

Code mode currently creates or updates both root files on every run. The preserve policy lets these repositories update openwiki/** without mutating their existing instruction layout, while retaining the current behavior by default.

Fixes #556.

Validation

• pnpm run format
• pnpm run lint
• pnpm run lint:check
• pnpm run typecheck
• pnpm run format:check
• targeted policy/command tests: 3 files, 99 tests passed
• full test run: 901 of 906 tests passed locally on Windows
  • the 3 Mermaid timeout failures passed when rerun in isolation (43 tests)
  • the remaining 2 failures are Windows environment limitations: symlink creation requires additional privileges, and the shell-backend test invokes the POSIX pwd command
• changeset status

[changeset-bot]

🦋 Changeset detected

Latest commit: e02a5b5

The changes in this PR will be included in the next version bump.

This PR includes changesets to release 1 package

Name	Type
openwiki	Minor

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