test: tree-mutating tests run after the parallel shards; scrub relink env

The flake family's root cause, finally: five test files REGENERATE
shared repo artifacts in place (catalog-mode-full rewrites every
SKILL.md in full-catalog mode; spec-sync and idempotency regenerate all
skills; gen-skill-docs and skill-validation rewrite .agents/). Any
concurrent shard reading those files sees a moving target — this one
family produced the exactly-doubled catalog estimate, the golden-file
drift, and the spec-sync mismatch chased earlier today. Full-suite mode
now runs TREE_MUTATING files in one serial shard AFTER the parallel
shards complete; CI's matrix is unaffected (per-runner checkouts).

Also: relink's run() helper spread process.env into its children, so a
sibling file's leaked GSTACK_HOME made the 'fresh install' test see a
neighbor's skill_prefix. GSTACK_HOME is now dropped unless the test
passes it explicitly.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

test/relink.test.ts

@@ -25,7 +25,15 @@ function run(cmd: string, env: Record<string, string> = {}, expectFail = false):
   try {
     return execSync(cmd, {
       cwd: ROOT,
-      env: { ...process.env, GSTACK_STATE_DIR: tmpDir, ...env },
+      // A sibling test file in the same shard PROCESS can leave GSTACK_HOME
+      // set on process.env; relink/config children must resolve state ONLY
+      // via the dirs this test passes (observed: 'fresh install' test saw a
+      // neighbor's skill_prefix and produced prefixed names).
+      env: (() => {
+        const child: Record<string, string | undefined> = { ...process.env, GSTACK_STATE_DIR: tmpDir, ...env };
+        if (!('GSTACK_HOME' in env)) delete child.GSTACK_HOME;
+        return child;
+      })(),
       encoding: 'utf-8',
       timeout: 10000,
       stdio: ['pipe', 'pipe', 'pipe'],