docs: rename patch tool to apply_patch and clarify apply_patch behavior

[yejiming]

Issue for this PR

Closes #19941

Type of change

• Bug fix
• New feature
• Refactor / code improvement
• Documentation

What does this PR do?

This PR fixes the built-in tool naming mismatch in the Tools docs.

Previously, the docs listed the patching tool as patch, but the actual registered tool ID is apply_patch. That mismatch caused plugin hooks checking input.tool === "patch" to never fire.

Changes made:

• Renamed the built-in tool section heading from patch to apply_patch.
• Updated permission notes to reference apply_patch instead of patch.
• Added explicit hook guidance to use input.tool === "apply_patch".
• Documented the apply_patch args shape:
  • Uses output.args.patchText
  • Does not expose output.args.filePath
  • Paths are embedded in marker lines and are relative to project root.

Why this works:

• It aligns documentation with the actual tool registry name in source.
• It prevents silent plugin hook failures due to incorrect tool ID checks.
• It clarifies how to parse file paths from patchText, matching runtime behavior.

How did you verify your code works?

• Reviewed and updated the relevant section in packages/web/src/content/docs/tools.mdx.
• Verified all changed references consistently use apply_patch.

Screenshots / recordings

Not applicable (documentation-only change).

Checklist

• I have tested my changes locally
• I have not included unrelated changes in this PR