feat: upgrade migration system — versioned fix scripts for broken state

Adds gstack-upgrade/migrations/ directory with version-keyed bash scripts
that run automatically during /gstack-upgrade (Step 4.75, after ./setup).
Each script is idempotent and handles state fixes that setup alone can't
cover. First migration: v0.15.2.0.sh runs gstack-relink to fix stale
directory symlinks from pre-v0.15.2.0 installs.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

gstack-upgrade/SKILL.md

@@ -170,6 +170,32 @@ mv "$LOCAL_GSTACK.bak" "$LOCAL_GSTACK"
 ```
 Tell user: "Sync failed — restored previous version at `$LOCAL_GSTACK`. Run `/gstack-upgrade` manually to retry."
 
+### Step 4.75: Run version migrations
+
+After `./setup` completes, run any migration scripts for versions between the old
+and new version. Migrations handle state fixes that `./setup` alone can't cover
+(stale config, orphaned files, directory structure changes).
+
+```bash
+MIGRATIONS_DIR="$INSTALL_DIR/gstack-upgrade/migrations"
+if [ -d "$MIGRATIONS_DIR" ]; then
+  for migration in $(find "$MIGRATIONS_DIR" -maxdepth 1 -name 'v*.sh' -type f 2>/dev/null | sort -V); do
+    # Extract version from filename: v0.15.2.0.sh → 0.15.2.0
+    m_ver="$(basename "$migration" .sh | sed 's/^v//')"
+    # Run if this migration version is newer than old version
+    # (simple string compare works for dotted versions with same segment count)
+    if [ "$OLD_VERSION" != "unknown" ] && [ "$(printf '%s\n%s' "$OLD_VERSION" "$m_ver" | sort -V | head -1)" = "$OLD_VERSION" ] && [ "$OLD_VERSION" != "$m_ver" ]; then
+      echo "Running migration $m_ver..."
+      bash "$migration" || echo "  Warning: migration $m_ver had errors (non-fatal)"
+    fi
+  done
+fi
+```
+
+Migrations are idempotent bash scripts in `gstack-upgrade/migrations/`. Each is named
+`v{VERSION}.sh` and runs only when upgrading from an older version. See CONTRIBUTING.md
+for how to add new migrations.
+
 ### Step 5: Write marker + clear cache
 
 ```bash

gstack-upgrade/SKILL.md.tmpl

@@ -168,6 +168,32 @@ mv "$LOCAL_GSTACK.bak" "$LOCAL_GSTACK"
 ```
 Tell user: "Sync failed — restored previous version at `$LOCAL_GSTACK`. Run `/gstack-upgrade` manually to retry."
 
+### Step 4.75: Run version migrations
+
+After `./setup` completes, run any migration scripts for versions between the old
+and new version. Migrations handle state fixes that `./setup` alone can't cover
+(stale config, orphaned files, directory structure changes).
+
+```bash
+MIGRATIONS_DIR="$INSTALL_DIR/gstack-upgrade/migrations"
+if [ -d "$MIGRATIONS_DIR" ]; then
+  for migration in $(find "$MIGRATIONS_DIR" -maxdepth 1 -name 'v*.sh' -type f 2>/dev/null | sort -V); do
+    # Extract version from filename: v0.15.2.0.sh → 0.15.2.0
+    m_ver="$(basename "$migration" .sh | sed 's/^v//')"
+    # Run if this migration version is newer than old version
+    # (simple string compare works for dotted versions with same segment count)
+    if [ "$OLD_VERSION" != "unknown" ] && [ "$(printf '%s\n%s' "$OLD_VERSION" "$m_ver" | sort -V | head -1)" = "$OLD_VERSION" ] && [ "$OLD_VERSION" != "$m_ver" ]; then
+      echo "Running migration $m_ver..."
+      bash "$migration" || echo "  Warning: migration $m_ver had errors (non-fatal)"
+    fi
+  done
+fi
+```
+
+Migrations are idempotent bash scripts in `gstack-upgrade/migrations/`. Each is named
+`v{VERSION}.sh` and runs only when upgrading from an older version. See CONTRIBUTING.md
+for how to add new migrations.
+
 ### Step 5: Write marker + clear cache
 
 ```bash

gstack-upgrade/migrations/v0.15.2.0.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+# Migration: v0.15.2.0 — Fix skill directory structure for unprefixed discovery
+#
+# What changed: setup now creates real directories with SKILL.md symlinks
+# inside instead of directory symlinks. The old pattern (qa -> gstack/qa)
+# caused Claude Code to auto-prefix skills as "gstack-qa" even with
+# --no-prefix, because Claude sees the symlink target's parent dir name.
+#
+# What this does: runs gstack-relink to recreate all skill entries using
+# the new real-directory pattern. Idempotent — safe to run multiple times.
+#
+# Affected: users who installed gstack before v0.15.2.0 with --no-prefix
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "$0")/../.." && pwd)"
+
+if [ -x "$SCRIPT_DIR/bin/gstack-relink" ]; then
+  echo "  [v0.15.2.0] Fixing skill directory structure..."
+  "$SCRIPT_DIR/bin/gstack-relink" 2>/dev/null || true
+fi