docs: add commit message formatting guidelines to AGENTS.md (JuliaLang#58629)

Add two additional guidelines for commit message formatting:
- When referencing external GitHub PRs or issues, use proper GitHub
  interlinking format (e.g., owner/repo#123)
- When fixing CI failures, include the link to the specific CI failure
  in the commit message

These guidelines help improve commit message clarity and traceability.

Author: Keno

AGENTS.md

@@ -51,6 +51,17 @@ corresponding test to ensure that the test is still passing with your changes.
 - Write one comment at the top of the test to explain what is being tested.
   Otherwise keep comments minimal.
 
+### External dependencies
+
+When modifying external dependencies (patches in `deps/patches/` or version updates in `deps/`):
+
+1. Always test builds with `USE_BINARYBUILDER=0` to ensure source builds work correctly
+2. For patches to external libraries:
+   - Verify the patch applies cleanly by running the extraction and patch steps
+   - Test the full build of the dependency: `make -C deps USE_BINARYBUILDER=0 compile-<depname>`
+   - Prefer using the full upstream commit in `git am` format (e.g., `git format-patch`) which includes proper commit metadata
+3. When updating dependency versions, ensure all associated patches still apply
+
 ### Writing code
 After writing code, look up the docstring for each function you used. If there
 are recommendations or additional considerations that apply to these functions,
@@ -69,6 +80,9 @@ documentation, etc., unless this is the main purpose of the change. Do not menti
 the test plan, unless it differs from what you were instructed to do in AGENTS.md.
 If your change fixes one or more issues, use the syntax "Fixes #" at the end of the commit message, but do not include it in the title.
 
+When referencing external GitHub PRs or issues, use proper GitHub interlinking format (e.g., `owner/repo#123` for PRs/issues).
+When fixing CI failures, include the link to the specific CI failure in the commit message.
+
 When creating pull requests, if the pull request consists of one commit only,
 use the body of the commit for the body of the pull request. If there are multiple
 commits in the pull request, follow the same guidelines for the pull request