GitHub does not report mutation-created issue-to-PR links through
closedByPullRequestsReferences(userLinkedOnly: true), so the
verification in `gh.py link-issue` failed even when
addCloseIssueReferences succeeded and the link existed.
Drop the re-query and trust the successful mutation: the command now
fails only when a link target is missing or the mutation does not
return the issue. Update the tests, the gh helper memory, the PR/issue
workflow memories, and the create-pr skill so they no longer promise
verification.
AI-assisted-by: deepseek-v4.1-flash
Add a link-issue command that creates GitHub's Development reference
and verifies both sides. Keep Closes in descriptions for context, but
make the API link the source of truth, including for merged PRs.
Add tests for successful links, missing verification, output, and
failures. Update the PR workflow memories and create-pr skill to use
the command.
AI-assisted-by: space-bunny-free
Move all development tools from tools/ to scripts/ for consistency.
Rename lint/fmt/check-fmt to lint-clj/fmt-clj/check-fmt-clj to clarify
they target Clojure specifically. Remove unused scripts (attach-opencode,
start-opencode, start-opencode-server) and the backport-commit skill.
Update all internal references across .serena/, AGENTS.md, and
CONTRIBUTING.md to point to the new script locations. Simplify
CONTRIBUTING.md by delegating module-specific fmt/lint instructions
to the respective serena memories.
AI-assisted-by: deepseek-v4-flash
