feat: add body modification flags and GraphQL mutations

[matleh]

Summary

Adds CLI flags and GraphQL mutations for partial body modifications, enabling agents to update bean content without direct file access. Builds on #59 (ETag support) and supersedes #57.

Changes

CLI: Body Modification Flags

• --body-replace-old / --body-replace-new for exact text replacement (must match exactly once)
• --body-append for appending content (supports stdin with -)
• Mutual exclusivity with existing --body/--body-file flags

GraphQL: Partial Body Mutations

• replaceInBody(id, old, new, ifMatch) - replace exactly one occurrence of text
• appendToBody(id, content, ifMatch) - append content with blank line separator
• Both support ifMatch for optimistic locking

Shared Logic

• Extract ReplaceOnce and AppendWithSeparator to internal/bean/content.go
• Reused by both CLI and GraphQL resolvers

Documentation

• Add GraphQL API section to README with examples

Usage

# CLI: Check off a task
beans update <id> --body-replace-old "- [ ] Task" --body-replace-new "- [x] Task"

# CLI: Append notes
beans update <id> --body-append "## Notes\n\nSome notes"

# GraphQL: Check off a task
beans query 'mutation { replaceInBody(id: "bean-xxx", old: "- [ ] Task", new: "- [x] Task") { body } }'

# GraphQL: Append content
beans query 'mutation { appendToBody(id: "bean-xxx", content: "## Notes") { body } }'

Why This Matters for Agents

Agents can now modify bean bodies entirely through CLI/GraphQL without needing:

• Direct file access to the .beans/ directory
• Knowledge of where beans are stored (which can be configured outside the repo)
• Special file permissions

Testing

• Comprehensive tests for shared logic in internal/bean/content_test.go
• GraphQL resolver tests for both mutations
• CLI tests updated for new behavior

[hmans]

Thanks for the PR, this is looking very good now. I've taken the liberty of removing the change in README.md, I hope you don't mind.

[hmans]

@matleh Had some unexpected merge conflicts when updating this branch with the latest stuff from main, can I ask you to do a quick check that everything is still intact & as intended?

[matleh]

@hmans I updated the branch and ran some manual tests to verify that the functionality works as expected.

[hmans]

Thank you! 🙏