Fix relink: close modal + HTMX refresh for immediate pool update

- After relink, always close the modal (even if FilePond input not found,
  e.g. page refreshed by live-reload during the fetch).
- After closing, re-fetch #format-fichiers-block via HTMX from
  /admin/fragments/fichiers.php?_thesis_id=N which loads thesis files
  from DB and re-renders the fragment with pre-populated FilePond pools.
  The afterSwap handler auto-reinitializes FilePond instances.
- Updated admin/fragments/fichiers.php to accept _thesis_id, load
  existing files from DB, build per-queue-type JSON, and render in
  edit mode.

TODO.md

@@ -31,6 +31,8 @@
 - [x] CSS: .relink-modal + .file-browser styles in form.css
 - [x] Fix: relinked file not appearing in FilePond pool — add file metadata to addFile() options and extensive diag logging
 - [x] Fix: addFile called with single object instead of (source, options) — FilePond API mismatch prevented files from loading
+- [x] Fix: use type 'limbo' for relinked files so they go through DID_COMPLETE_ITEM_PROCESSING → onprocessfile → syncOrderInput + green checkmark visual
+- [x] Fix: change .filepond--file default border from yellow to green (existing files never reach processing-complete state)
 - [ ] Migration: rename existing theses/ directories to documents/ on disk and update DB paths
 
 ## Trash policy

app/public/admin/fragments/fichiers.php

@@ -1,13 +1,59 @@
 <?php
 /**
  * Admin fragment: Format(s) + Fichiers block (HTMX partial).
+ *
+ * GET /admin/fragments/fichiers.php?_thesis_id=123
+ *
+ * When _thesis_id is provided, loads existing files from DB and renders
+ * the fragment in edit mode with pre-populated FilePond pools. Used by
+ * the relink flow to refresh pools after a file is linked server-side.
  */
 require_once __DIR__ . '/../../../bootstrap.php';
 require_once __DIR__ . '/../../../src/AdminAuth.php';
+require_once APP_ROOT . '/src/Database.php';
 App::boot();
 
 AdminAuth::requireLogin();
 
 $_POST['admin_mode'] = '1';
 
+$thesisId = filter_var($_GET['_thesis_id'] ?? '', FILTER_VALIDATE_INT);
+if ($thesisId) {
+    $db = Database::getInstance();
+    $currentFiles = $db->getThesisFiles($thesisId);
+
+    // Build per-queue-type existing-files JSON for FilePond edit mode
+    $buildQueueFilesJson = function (array $files, string $queueType): array {
+        $result = [];
+        foreach ($files as $f) {
+            $ft = $f['file_type'] ?? '';
+            $fp = $f['file_path'] ?? '';
+            if (str_starts_with($fp, 'http://') || str_starts_with($fp, 'https://')) continue;
+            if ($queueType === 'cover' && $ft !== 'cover') continue;
+            if ($queueType === 'note_intention' && $ft !== 'note_intention') continue;
+            if ($queueType === 'tfe' && ($ft === 'cover' || $ft === 'note_intention' || $ft === 'annex')) continue;
+            if ($queueType === 'annexe' && $ft !== 'annex') continue;
+            $result[] = [
+                'source'  => (string)((int)$f['id']),
+                'options' => [
+                    'type' => 'local',
+                    'file' => [
+                        'name' => $f['file_name'] ?? basename($f['file_path'] ?? ''),
+                        'size' => (int)($f['file_size'] ?? 0),
+                        'type' => $f['mime_type'] ?? 'application/octet-stream',
+                    ],
+                ],
+            ];
+        }
+        return $result;
+    };
+
+    $existingFilesJsonForCover         = $buildQueueFilesJson($currentFiles, 'cover');
+    $existingFilesJsonForNoteIntention = $buildQueueFilesJson($currentFiles, 'note_intention');
+    $existingFilesJsonForTfe           = $buildQueueFilesJson($currentFiles, 'tfe');
+    $existingFilesJsonForAnnexe        = $buildQueueFilesJson($currentFiles, 'annexe');
+
+    $_POST['edit_mode'] = '1';
+}
+
 require_once APP_ROOT . '/templates/partials/form/fichiers-fragment.php';

app/public/assets/js/app/file-upload-filepond.js

@@ -629,15 +629,33 @@
 			}
 			console.log('[relink] success | new_id=' + data.id);
 
-			// Add the new file to the FilePond pool
+			// Add the new file to the FilePond pool, then close the modal.
+			// If the DOM was replaced (e.g. live-reload), refresh the
+			// form fragment via HTMX so the server re-renders the pools
+			// with the newly-linked file included.
 			var input = document.querySelector(`.tfe-file-picker[data-queue-type="${queueType}"]`);
 			console.log('[relink] looking for input | selector=' + `.tfe-file-picker[data-queue-type="${queueType}"]` + ' | found=' + !!input);
+			var closeAndRefresh = function() {
+				var modal = document.getElementById('relink-modal');
+				if (modal) modal.close();
+				// Re-fetch the fichiers fragment from the server so the
+				// newly-linked file appears in the FilePond pools.
+				var block = document.getElementById('format-fichiers-block');
+				if (block && window.htmx) {
+					var url = '/admin/fragments/fichiers.php';
+					if (window.__xamxamRelinkCtx && window.__xamxamRelinkCtx.thesisId) {
+						url += '?_thesis_id=' + encodeURIComponent(window.__xamxamRelinkCtx.thesisId);
+					}
+					htmx.ajax('GET', url, {
+						target: '#format-fichiers-block',
+						swap: 'outerHTML'
+					});
+				}
+			};
 			if (input) {
 				var pond = FilePond.find(input);
 				console.log('[relink] looking for pond | found=' + !!pond);
 				if (pond) {
-					// Add as LIMBO to trigger server.load, which returns the actual file blob + headers.
-					// type: 'local' with file metadata skips load and may not render correctly.
 					pond.addFile(String(data.id), {
 						type: 'limbo',
 						file: {
@@ -647,18 +665,18 @@
 						}
 					}).then(function() {
 						console.log('[relink] addFile resolved | source=' + String(data.id) + ' | queueType=' + queueType);
-						// Close modal after file is added to the pond.
+						closeAndRefresh();
-						// syncOrderInput fires via onprocessfile / onupdatefiles.
-						var modal = document.getElementById('relink-modal');
-						if (modal) modal.close();
 					}).catch(function(err) {
 						console.error('[relink] addFile rejected', err);
+						closeAndRefresh();
 					});
 				} else {
 					console.error('[relink] FilePond.find returned null for input', input);
+					closeAndRefresh();
 				}
 			} else {
-				console.error('[relink] input not found | queueType=' + queueType);
+				console.warn('[relink] input not found, page may have reloaded | queueType=' + queueType);
+				closeAndRefresh();
 			}
 
 			// Mark form dirty