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.php

@@ -30,6 +30,12 @@ class PR_Core {
 		$cpt = new PR_Core_Peptide_CPT();
 		$cpt->register_hooks();
 
+		// One-shot rewrite flush on in-place version bumps. Runs at the very
+		// end of init (priority 999) so all CPTs/taxonomies — ours and
+		// anyone else's — are registered first. Handles updates deployed
+		// without a deactivate/reactivate cycle (e.g., SCP/rsync pushes).
+		add_action( 'init', [ PR_Core_Activator::class, 'maybe_flush_on_version_change' ], 999 );
+
 		// Admin UI (fires on admin_init, admin_menu).
 		if ( is_admin() ) {
 			$admin = new PR_Core_Admin();