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

Resolves the rewrite slug collision that was 404'ing all 89 production
peptide detail pages. PR Core v0.1.1 registered an empty pr_peptide CPT
claiming /peptides/%postname%/; WP's rewrite resolver picked it over PSA's
populated peptide CPT. This release consolidates both registrations onto a
single peptide CPT owned by PR Core. PSA v4.5.0 drops its registration in
favor of this one.

## Contract (per CTO msg 02)
- POST_TYPE: pr_peptide -> peptide
- TAX_CATEGORY: pr_peptide_category -> peptide_category
- TAX_FAMILY const removed (pr_peptide_family was never populated)
- CPT + taxonomy registration guarded with post_type_exists() / taxonomy_exists()
  so deploy order between PR Core and PSA is forgiving
- Args harmonized as superset of PSA + prior PR Core (thumbnail added to
  supports; capability_type + map_meta_cap preserved)
- Activator: flush_rewrite_rules(false) on activation; new
  maybe_flush_on_version_change() handler hooked at init:999 for in-place
  updates that bypass the activation hook (e.g. SCP deploys)
- uninstall.php: blanket DELETE replaced with JOIN on _pr_core_authored so
  PSA-authored peptide posts (the 89 canonical monographs) are never destroyed;
  peptide_category terms preserved (shared ownership)
- Scrub scope: narrow — CPT-slug-derived identifiers only; class names,
  file names, PR_CORE_* constants, pr_core_* options, and pr-core/v1 REST
  namespace remain

## Docs
- ARCHITECTURE.md: new Key Decision #7 (v0.2.0 consolidation) and §2.9
  Uninstall specification
- CONVENTIONS.md: CPT Ownership rule + _pr_core_authored flag contract

## Tests
- Lightweight harness (tests/bootstrap.php) that stubs the handful of WP
  functions exercised by the CPT class
- tests/unit/test-peptide-cpt.php asserts: constants match contract,
  TAX_FAMILY is removed, guard no-ops when post_type_exists/taxonomy_exists
  returns true, args payload shape (thumbnail in supports, rewrite slug,
  REST namespace), hooks wired
- CI: new 'Unit tests (lightweight, no PHPUnit)' step in lint-php job,
  runs across PHP 8.1/8.2/8.3. Full PHPUnit + wp-env harness is a
  follow-up

Refs: convo/prcore/threads/2026-04-peptides-cpt-collision/02-cto-correction.md

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 );
 	}
 
 	/**