feat(cpt): consolidate peptide CPT with PSA; drop pr_peptide (v0.2.0) (#1)

Consolidates the `peptide` CPT under PR Core ownership, dropping the `pr_peptide` slug-collision that was 404ing all 89 peptide detail pages.

- POST_TYPE: pr_peptide -> peptide
- TAX_CATEGORY: pr_peptide_category -> peptide_category
- TAX_FAMILY + pr_peptide_family taxonomy removed
- Defensive post_type_exists/taxonomy_exists guards on both registrations
- Args harmonized as superset of PSA + prior PR Core (adds thumbnail support)
- Activation hook + init:999 version-change flush handler
- Uninstall scoped to _pr_core_authored flag (PSA-authored posts survive)
- Plugin version 0.1.1 -> 0.2.0, CHANGELOG in same commit
- ARCHITECTURE.md + CONVENTIONS.md updated with CPT ownership rule

QA gate verdict: PASS (qa-reviews/peptide-repo-core/2026-04-22-874f93b.md)
Sibling release: peptiderepo/peptide-search-ai#15 (PSA v4.5.0)

Known follow-up: manage_peptide_content capability is not granted to any role as of v0.2.0. No current UI/theme reads or writes PR Core-defined meta keys, so no regression. Follow-up thread to decide role assignment.

includes/class-pr-core-activator.php

@@ -5,17 +5,26 @@ declare(strict_types=1);
  * Plugin activation handler.
  *
  * What: Runs migrations, adds capabilities, flushes rewrite rules.
- * Who calls it: register_activation_hook() in peptide-repo-core.php.
- * Dependencies: PR_Core_Migration_Runner.
+ *       Also detects version changes on subsequent init cycles and re-flushes
+ *       rewrite rules once so in-place plugin updates (without a deactivate +
+ *       reactivate cycle) still pick up CPT/taxonomy slug changes.
+ * Who calls it: register_activation_hook() in peptide-repo-core.php; and
+ *               PR_Core::init() registers maybe_flush_on_version_change on init:999.
+ * Dependencies: PR_Core_Migration_Runner, PR_Core_Peptide_CPT.
  *
  * @see peptide-repo-core.php — Registers this class on activation.
+ * @see includes/class-pr-core.php — Wires the init:999 version-change handler.
  */
 class PR_Core_Activator {
 
+	/** @var string Option key storing the last activated/seen plugin version. */
+	private const VERSION_OPTION = 'pr_core_version';
+
 	/**
 	 * Run on plugin activation.
 	 *
-	 * Side effects: database table creation, capability grants, rewrite flush.
+	 * Side effects: database table creation, capability grants, rewrite flush,
+	 *               pr_core_version option write.
 	 *
 	 * @return void
 	 */
@@ -32,7 +41,39 @@ class PR_Core_Activator {
 		self::add_capabilities();
 
 		// Flush rewrite rules for the new CPT.
-		flush_rewrite_rules();
+		flush_rewrite_rules( false );
+
+		// Record the activated version so the init:999 drift handler can
+		// detect future in-place updates and re-flush without a manual
+		// deactivate/reactivate cycle.
+		update_option( self::VERSION_OPTION, PR_CORE_VERSION, false );
+	}
+
+	/**
+	 * Detect in-place plugin version changes and flush rewrite rules once.
+	 *
+	 * Wired to init:999 so all CPTs + taxonomies (ours and anyone else's)
+	 * are registered before the flush. When the option is absent (first
+	 * install that bypassed the activation hook — e.g., manual SCP deploy)
+	 * or is older than the current constant, we flush once and update.
+	 *
+	 * Side effects: may call flush_rewrite_rules( false ); updates option.
+	 *
+	 * @return void
+	 */
+	public static function maybe_flush_on_version_change(): void {
+		if ( ! defined( 'PR_CORE_VERSION' ) ) {
+			return;
+		}
+
+		$recorded = get_option( self::VERSION_OPTION, '' );
+
+		if ( PR_CORE_VERSION === $recorded ) {
+			return;
+		}
+
+		flush_rewrite_rules( false );
+		update_option( self::VERSION_OPTION, PR_CORE_VERSION, false );
 	}
 
 	/**