feat: initial peptide-repo-core plugin (v0.1.0) — canonical schema sprint

Implements ADR-0002: canonical peptide schema as shared data layer for
the peptiderepo.com ecosystem. All Tier 1 tools (Reconstitution Calculator,
Dosage Reference, Legal Status Tracker, PSA enhancements) build on this.

Includes:
- pr_peptide CPT with REST, taxonomies, 11 meta fields
- 3 custom tables: pr_dosing_rows, pr_legal_cells, pr_ai_candidate_queue
- Sequential migration runner with schema versioning
- 4 typed DTOs and 4 repository classes (full CRUD)
- REST API (pr-core/v1): 6 endpoints (read public, write auth-gated)
- Admin UI: 3 meta boxes, custom columns, AI candidate queue page
- Shared disclaimer component (shortcode + static API)
- JSON-LD Drug schema emission on single peptide pages
- Seed data fixture (3 peptides, 10 dosing rows, 5 legal cells)
- Full teardown in uninstall.php
- CI: PHP lint 8.0-8.2, PHPCS WordPress, 300-line check

All 22 PHP files under 300 lines. Highest: peptide-cpt at 265.

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

includes/migrations/class-pr-core-migration-runner.php

@@ -0,0 +1,97 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Schema migration runner.
+ *
+ * What: Compares current schema version against target, runs pending migrations.
+ * Who calls it: PR_Core::init() on every plugins_loaded, PR_Core_Activator on activation.
+ * Dependencies: WordPress $wpdb, dbDelta().
+ *
+ * Migrations are numbered sequentially (0001, 0002, ...). Each migration class
+ * must implement up() and optionally down(). All migrations are idempotent.
+ *
+ * @see peptide-repo-core.php — Defines PR_CORE_TARGET_SCHEMA_VERSION.
+ * @see CONVENTIONS.md        — "How To: Add a New Migration".
+ */
+class PR_Core_Migration_Runner {
+
+	/** @var string Option key storing current schema version. */
+	private const VERSION_OPTION = 'pr_core_schema_version';
+
+	/**
+	 * Ordered list of migration classes.
+	 * Index 0 = migration 1 (bumps schema to version 1).
+	 *
+	 * @var string[]
+	 */
+	private const MIGRATIONS = [
+		'PR_Core_Migration_0001_Dosing_Rows',
+		'PR_Core_Migration_0002_Legal_Cells',
+		'PR_Core_Migration_0003_Candidate_Queue',
+	];
+
+	/**
+	 * Run all pending migrations up to PR_CORE_TARGET_SCHEMA_VERSION.
+	 *
+	 * Side effects: creates/alters database tables, updates schema version option.
+	 *
+	 * @return void
+	 */
+	public function run_pending(): void {
+		$current = (int) get_option( self::VERSION_OPTION, 0 );
+		$target  = PR_CORE_TARGET_SCHEMA_VERSION;
+
+		if ( $current >= $target ) {
+			return;
+		}
+
+		require_once ABSPATH . 'wp-admin/includes/upgrade.php';
+
+		for ( $i = $current; $i < $target; $i++ ) {
+			if ( ! isset( self::MIGRATIONS[ $i ] ) ) {
+				break;
+			}
+
+			$class = self::MIGRATIONS[ $i ];
+			if ( ! class_exists( $class ) ) {
+				// Migration file not autoloaded — load explicitly.
+				$file = $this->class_to_file( $class );
+				if ( file_exists( $file ) ) {
+					require_once $file;
+				}
+			}
+
+			if ( class_exists( $class ) ) {
+				$migration = new $class();
+				$migration->up();
+			}
+
+			update_option( self::VERSION_OPTION, $i + 1 );
+		}
+	}
+
+	/**
+	 * Get current schema version.
+	 *
+	 * @return int
+	 */
+	public function get_current_version(): int {
+		return (int) get_option( self::VERSION_OPTION, 0 );
+	}
+
+	/**
+	 * Convert migration class name to file path.
+	 *
+	 * PR_Core_Migration_0001_Dosing_Rows => migrations/class-pr-core-migration-0001-dosing-rows.php
+	 *
+	 * @param string $class Fully-qualified class name.
+	 * @return string Absolute file path.
+	 */
+	private function class_to_file( string $class ): string {
+		$suffix = substr( $class, 8 ); // Strip 'PR_Core_'.
+		$filename = 'class-pr-core-' . str_replace( '_', '-', strtolower( $suffix ) ) . '.php';
+
+		return PR_CORE_PLUGIN_DIR . 'includes/migrations/' . $filename;
+	}
+}