Declare agent tool runtime metadata

[chubes4]

Summary

• Declares Data Machine agent-loop runtime metadata on Data Machine Code tool definitions.
• Marks workspace/GitHub/WordPress inspection tools as repeatable so duplicate-call prevention does not block legitimate re-reads.
• Marks workspace mutations, GitHub writes, PR creation, and issue creation as progress signals for completion assertion nudges.

Depends on Extra-Chill/data-machine#1951.

Testing

• php -l inc/Tools/WorkspaceTools.php
• php -l inc/Tools/GitHubTools.php
• php -l inc/Tools/WordPressRuntimeTools.php
• php -l inc/Tools/GitHubPullRequestTool.php
• php -l inc/Tools/GitHubIssueTool.php
• php -l inc/Tools/WorkspaceDiffTools.php
• php tests/smoke-tool-result-contracts.php
• git diff --check

AI assistance

• AI assistance: Yes
• Tool(s): OpenCode (GPT-5.5)
• Used for: Drafted the tool metadata declarations and validation pass based on the Data Machine runtime metadata contract.