fix(#705): route hardcoded $HOME gsd-tools invocations in agents/commands through gsd_run (#707)

* fix(#705): route hardcoded $HOME gsd-tools invocations in agents/commands through gsd_run

The hardcoded `node "$HOME/.claude/gsd-core/bin/gsd-tools.cjs" <cmd>` form
(fixed for workflows in #621/#637) survived in agent/command surfaces and
misresolves on global/shim-only installs. Route every agent-executed
invocation through the resolved `gsd_run` launcher in gsd-phase-researcher,
gsd-planner (load_graph_context extracted to a shared reference to stay under
the planner size budget), import, and graphify. Add a regression guard over
agents/ + commands/ + gsd-core/references/ bash blocks. User-facing display
messages and docs are intentionally left untouched.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

* fix(#705): use repo changeset fragment format (type: Fixed, pr: 707)

The hand-written fragment used the standard changesets package format
(package: bump) which lacks the type:/pr: frontmatter the repo's
docs-required lint consumes (fail_malformed_fragment / missing_type).
Regenerated via scripts/changeset/new.cjs.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

tests/bug-622-graphify-optional-graph-html.test.cjs

@@ -41,8 +41,9 @@ const GRAPHIFY_MD = path.join(__dirname, '..', 'commands', 'gsd', 'graphify.md')
  */
 function extractStep3Block() {
   const content = fs.readFileSync(GRAPHIFY_MD, 'utf-8');
-  // Capture from the `graphify update .` line through the next closing ``` fence.
-  const match = content.match(/```bash\r?\n(graphify update \.[^\0]*?)```/);
+  // Capture the full body of the ```bash fence that CONTAINS `graphify update .`
+  // (including any leading preamble line), without crossing into other fences.
+  const match = content.match(/```bash\r?\n((?:(?!```)[\s\S])*?graphify update \.(?:(?!```)[\s\S])*?)\r?\n```/);
   return match ? match[1].trim() : null;
 }