Reimplement issue dependencies on go-github v89 REST API

[tommaso-moro]

Summary

Switches the issue_dependency_read / issue_dependency_write tools from the GraphQL (githubv4) implementation to the first-class REST methods added in go-github v89.

📚 Stacked on #2840 (the go-github v87 → v89 bump). Review/merge that first; this PR targets its branch and the diff here is just the feature change.

Why

Issue dependencies (added in #2751) were built on GraphQL via githubv4. Because the pinned githubv4 library predates the dependency mutations, the code had to hand-declare AddBlockedByInput / RemoveBlockedByInput and resolve issue numbers to node IDs with a custom aliased query. go-github v89 now exposes maintained, typed REST methods (ListBlockedBy, ListBlocking, AddBlockedBy, RemoveBlockedBy), so the tools can drop the workaround and align with the rest of the REST-based issue tooling.

Refs #950 (original feature request; the capability itself already shipped in #2751 — this PR is a cleanup onto the public REST API).

What changed

• Rewrite issue_dependencies.go on REST: page-based pagination for reads, and a single Issues.Get to resolve the blocking issue's database ID for writes. Tool names, methods, the self-dependency guard, and cross-repo support are all preserved.
• Rewrite the issue-dependency tests on the REST mock helpers (drop githubv4mock for this file).
• Regenerate the read toolsnap (cursor → page pagination) and the feature-flag docs.

MCP impact

• Tool schema or behavior changed
  • issue_dependency_read pagination changes from cursor-based (after) to standard REST page-based (page / perPage), matching other list tools. issue_dependency_write behavior is unchanged. Both remain gated behind the issue_dependencies feature flag.

Prompts tested (tool changes only)

Covered by unit tests against the REST mock (both tools are feature-flagged; not exercised via live e2e here):

• "What issues block issue Issue: Fix incorrect VS Code installation URL (both buttons point to Insiders) #123 in owner/repo?" → issue_dependency_read / get_blocked_by
• "Which issues does Issue: Fix incorrect VS Code installation URL (both buttons point to Insiders) #123 block?" → issue_dependency_read / get_blocking
• "Mark issue Issue: Fix incorrect VS Code installation URL (both buttons point to Insiders) #123 as blocked by Bump go-github to v72.0.0 #456" → issue_dependency_write / add + blocked_by
• "Remove the dependency where Issue: Fix incorrect VS Code installation URL (both buttons point to Insiders) #123 blocks Bump go-github to v72.0.0 #456" → issue_dependency_write / remove + blocking

Security / limits

• Auth / permissions considered
  • Same repo scope and behavior as before; no change to data exposure. Dependency tools stay behind the issue_dependencies feature flag.

Tool renaming

• I am not renaming tools as part of this PR

Lint & tests

• Linted locally with ./script/lint
• Tested locally with ./script/test

Docs

• Updated (README / docs / examples)