fix(tests): guard error_log/wp_json_encode stubs + document idempotency limitation

- tests/unit/test-migration-0004.php: wrap error_log() stub in
  function_exists() guard -- prevents PHP fatal redeclaration on
  PHP Lint (8.1/8.2/8.3) which runs php -l on all .php files.

- tests/bootstrap.php: update wp_json_encode stub to accept
  int $flags = 0 second arg (matches production call signature
  wp_json_encode($clean, JSON_UNESCAPED_UNICODE)); guard with
  function_exists().

- class-pr-core-migration-0004-backfill-peptide-meta.php: add
  code comment near idempotency check documenting the all-or-nothing
  limitation (post with legitimately empty aliases will re-run).

- CONVENTIONS.md: one-line note under migration conventions item 5
  documenting the idempotency caveat.

- CHANGELOG.md: add Fixed section under v0.6.0 for CI/test-stub fix.

Agent-Session: peptide-schema-backfill v0.6.0 P1 fix

CHANGELOG.md

@@ -30,6 +30,10 @@ Format: [Semantic Versioning](https://semver.org/).
 - `ARCHITECTURE.md` — §#6 JSON-LD rewritten; §2.9 uninstall spec updated; file tree updated for new classes.
 - `CONVENTIONS.md` — schema-input meta convention added; Yoast JSON-LD extension pattern added.
 
+### Fixed
+- `tests/unit/test-migration-0004.php`: `error_log()` stub now guarded with `function_exists()` to prevent PHP fatal redeclaration error in CI PHP Lint (8.1/8.2/8.3).
+- `tests/bootstrap.php`: `wp_json_encode` stub updated to accept `int $flags = 0` second argument, matching production call signature; guarded with `function_exists()`.
+
 ### Technical
 - Schema version: `PR_CORE_TARGET_SCHEMA_VERSION` = 4.
 - New test files: `tests/unit/test-migration-0004.php`, `tests/unit/test-jsonld.php`.

CONVENTIONS.md

@@ -38,6 +38,7 @@ Files live in `includes/` or one level of subdirectory under `includes/`.
 3. Add the class name to `PR_Core_Migration_Runner::MIGRATIONS` array (index = version - 1).
 4. Bump `PR_CORE_TARGET_SCHEMA_VERSION` in `peptide-repo-core.php`.
 5. All migrations must be idempotent (safe to run twice).
+6. **Idempotency caveat (all-or-nothing skip):** migration 0004's skip guard requires *all* populated keys; a post with legitimately empty aliases will re-run on manual re-invoke — this is safe (write_meta only overwrites with non-empty values) but expected.
 
 ## How To: Add a New REST Endpoint
 

includes/migrations/class-pr-core-migration-0004-backfill-peptide-meta.php

@@ -93,6 +93,11 @@ class PR_Core_Migration_0004_Backfill_Peptide_Meta {
 		$existing_weight  = (string) get_post_meta( $post_id, self::META_WEIGHT, true );
 		$existing_aliases = (string) get_post_meta( $post_id, self::META_ALIASES, true );
 
+		// Idempotency limitation: this guard is all-or-nothing. A peptide that legitimately
+		// has no aliases (e.g., a novel compound) will never satisfy all three conditions and
+		// the migration will re-run on every manual re-invoke. This is safe because
+		// write_meta_from_psa() / write_meta_from_pubchem() only overwrite with non-empty
+		// values, but callers should be aware the 'skipped' result requires all three keys set.
 		if ( '' !== $existing_formula && '' !== $existing_weight && '' !== $existing_aliases ) {
 			return 'skipped';
 		}

tests/bootstrap.php

@@ -113,8 +113,10 @@ function sanitize_text_field( $value ): string {
 	return is_scalar( $value ) ? trim( (string) $value ) : '';
 }
 
-function wp_json_encode( $data ): string {
-	return json_encode( $data ) ?: '[]';
+if ( ! function_exists( 'wp_json_encode' ) ) {
+	function wp_json_encode( $data, int $flags = 0 ): string {
+		return json_encode( $data, $flags ) ?: '[]';
+	}
 }
 
 function absint( $value ): int {

tests/unit/test-migration-0004.php

@@ -71,9 +71,11 @@ function esc_html( string $val ): string {
 	return htmlspecialchars( $val, ENT_QUOTES, 'UTF-8' );
 }
 
-function error_log( string $msg ): bool {
-	// Suppress during tests.
-	return true;
+if ( ! function_exists( 'error_log' ) ) {
+	function error_log( string $msg ): bool {
+		// Suppress during tests.
+		return true;
+	}
 }
 
 // Load dependencies.