fix: auto-regenerate thesis identifier on any year-prefix mismatch, support .php migrations in runner

ThesisEditController::save() previously only regenerated the identifier when
the year field changed during an edit. If a thesis had its year corrected in
a past edit (or via other means) and the identifier still carried the old
year prefix, subsequent edits that didn't touch the year field would leave
the mismatched identifier in place.

Now saves() also checks whether the existing identifier's 4-digit prefix
matches the thesis year, and regenerates if not — regardless of whether year
changed in the current edit.

The migration runner (run.php) only scanned for .sql files, so PHP migrations
(013, 016, 018, 038) were never auto-applied. Extended the runner to also
discover and execute .php migrations in a subprocess. If a PHP migration fails
with an idempotent error (no such column, already exists, duplicate column),
the runner treats it as already-applied and continues rather than aborting
— preventing a stale migration like 016 (banner_path already dropped by 028)
from blocking migrations that come after it alphabetically (e.g. 038).

Updated migrations 016 and 038 to accept an optional $argv[1] DB path.
Fixed 016 to gracefully handle the banner_path column already being gone
(exit 0 instead of fatal).

TODO.md

@@ -12,4 +12,11 @@
 - [x] Migration 038: corriger les identifiers theses qui ne matchent pas leur année
 - [x] Filtres finalité + format dans la page de recherche (search.php)
 - [x] Styliser boutons Filtrer/Réinitialiser : plus compacts, Réinitialiser en neutre
-- [ ] Commit + jj new
+- [x] Commit + jj new
+
+- [x] Fix identifier-year mismatch: extend save() to regenerate identifier when prefix doesn't match year (not just on year change)
+- [x] Fix migration runner run.php to support .php migrations alongside .sql
+- [x] Fix runner: treat PHP subprocess idempotent errors (no such column / already exists) as skippable rather than fatal
+- [x] Update 016 and 038 PHP migrations to accept $argv[1] DB path
+- [x] Fix migration 016 to gracefully handle banner_path column already being dropped
+- [x] Commit + jj new

app/migrations/applied/016_merge_banners_into_covers.php

@@ -15,7 +15,8 @@
 defined('APP_ROOT') || define('APP_ROOT', dirname(__DIR__, 2));
 defined('STORAGE_ROOT') || define('STORAGE_ROOT', APP_ROOT . '/storage');
 
-$dbPath = APP_ROOT . '/storage/xamxam.db';
+// Accept optional DB path from command line (used by run.php runner)
+$dbPath = $argv[1] ?? (APP_ROOT . '/storage/xamxam.db');
 if (!file_exists($dbPath)) {
     echo "ERROR: database not found at $dbPath\n";
     exit(1);
@@ -34,9 +35,17 @@ if (!is_dir($coverDir)) {
     echo "Created covers/ directory.\n";
 }
 
-// Fetch all theses with a non-null banner_path
+// Detect if banner_path column still exists (dropped by migration 028)
+try {
     $stmt = $pdo->query("SELECT id, banner_path FROM theses WHERE banner_path IS NOT NULL");
     $rows = $stmt->fetchAll();
+} catch (\PDOException $e) {
+    if (stripos($e->getMessage(), 'no such column') !== false) {
+        echo "banner_path column already removed — migration 016 already applied, nothing to do.\n";
+        exit(0);
+    }
+    throw $e;
+}
 
 if (empty($rows)) {
     echo "No banners to migrate.\n";

app/migrations/applied/038_fix_mismatched_identifiers.php

@@ -19,7 +19,8 @@
 defined('APP_ROOT') || define('APP_ROOT', dirname(__DIR__, 2));
 defined('STORAGE_ROOT') || define('STORAGE_ROOT', APP_ROOT . '/storage');
 
-$dbPath = APP_ROOT . '/storage/xamxam.db';
+// Accept optional DB path from command line (used by run.php runner)
+$dbPath = $argv[1] ?? (APP_ROOT . '/storage/xamxam.db');
 if (!file_exists($dbPath)) {
     echo "ERROR: database not found at $dbPath\n";
     exit(1);

app/migrations/run.php

@@ -38,11 +38,11 @@ if (!is_dir($appliedDir)) {
     mkdir($appliedDir, 0755, true);
 }
 
-// Collect .sql files from both pending and applied dirs
+// Collect .sql and .php files from both pending and applied dirs
 $files = [];
 foreach ([$pendingDir, $appliedDir] as $dir) {
     if (!is_dir($dir)) continue;
-    foreach (glob($dir . '/*.sql') as $f) {
+    foreach (glob($dir . '/*.{sql,php}', GLOB_BRACE) as $f) {
         $files[basename($f)] = $f;
     }
 }
@@ -61,12 +61,51 @@ foreach ($files as $name => $file) {
         continue;
     }
 
+    $ext = strtolower(pathinfo($name, PATHINFO_EXTENSION));
     echo "Applying: $name\n";
-    $sql = file_get_contents($file);
+
+    $isPhp = $ext === 'php';
 
     try {
+        if ($isPhp) {
+            // PHP migrations: execute in a subprocess for isolation
+            $cmd = sprintf(
+                'php %s %s 2>&1',
+                escapeshellarg($file),
+                escapeshellarg($dbPath)
+            );
+            exec($cmd, $output, $exitCode);
+            $outputStr = implode("\n", $output);
+            echo $outputStr . "\n";
+            if ($exitCode !== 0) {
+                // Check output for idempotent errors before treating as fatal
+                $skipPatterns = [
+                    'no such column',
+                    'duplicate column name',
+                    'already exists',
+                ];
+                $shouldSkip = false;
+                foreach ($skipPatterns as $pat) {
+                    if (stripos($outputStr, $pat) !== false) {
+                        $shouldSkip = true;
+                        break;
+                    }
+                }
+                if ($shouldSkip) {
+                    echo "  Skipping (already applied)\n";
+                    // Mark as applied so we don't re-attempt
+                    $pdo->prepare("INSERT OR REPLACE INTO _migrations (name) VALUES (?)")->execute([$name]);
+                    $count++;
+                    continue;
+                }
+                throw new RuntimeException("PHP migration exited with code $exitCode");
+            }
+        } else {
+            // SQL migrations: execute inline
+            $sql = file_get_contents($file);
             $pdo->exec($sql);
-    } catch (PDOException $e) {
+        }
+    } catch (\Throwable $e) {
         $msg = $e->getMessage();
         // Ignore idempotent errors (column/trigger/index already exists or already removed)
         if (stripos($msg, 'duplicate column name') !== false

app/src/Controllers/ThesisEditController.php

@@ -220,14 +220,19 @@ class ThesisEditController
                 'cc2r'            => !empty($post['cc2r']),
                 'license_custom'  => trim($post['license_custom'] ?? ''),
             ];
-            // Regenerate identifier if year changed
+            // Regenerate identifier if year changed or if identifier prefix doesn't match year
             $oldThesis = $this->db->getThesis($thesisId);
             $oldYear = (int)($oldThesis['year'] ?? 0);
             $newYear = $meta['year'];
-            if ($newYear !== $oldYear && $newYear >= 2000) {
+            $oldIdentifier = $oldThesis['identifier'] ?? '';
+            $oldIdentifierYear = ($oldIdentifier !== '' && preg_match('/^(\d{4})/', $oldIdentifier, $m)) ? (int)$m[1] : 0;
+            if ($newYear >= 2000 && ($newYear !== $oldYear || $oldIdentifierYear !== $newYear)) {
                 $newIdentifier = $this->db->generateThesisIdentifier($newYear);
                 $meta['identifier'] = $newIdentifier;
-                error_log('[ThesisEdit] Year changed ' . $oldYear . ' → ' . $newYear . ', new identifier: ' . $newIdentifier);
+                $reason = $newYear !== $oldYear
+                    ? 'Year changed ' . $oldYear . ' → ' . $newYear
+                    : 'Mismatched identifier ' . $oldIdentifier . ' for year=' . $newYear;
+                error_log('[ThesisEdit] ' . $reason . ', new identifier: ' . $newIdentifier);
             }
 
             $this->db->updateThesis($thesisId, $meta);