feat: implement SQLite backup & data integrity plan (Phases 2-4)

app/storage/schema.sql

@@ -84,7 +84,8 @@ INSERT OR IGNORE INTO finality_types (name) VALUES
 CREATE TABLE IF NOT EXISTS languages (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     name TEXT NOT NULL UNIQUE,
-    created_at DATETIME DEFAULT CURRENT_TIMESTAMP
+    created_at DATETIME DEFAULT CURRENT_TIMESTAMP,
+    deleted_at TEXT DEFAULT NULL
 );
 
 INSERT OR IGNORE INTO languages (name) VALUES
@@ -112,7 +113,8 @@ INSERT OR IGNORE INTO format_types (name) VALUES
 CREATE TABLE IF NOT EXISTS tags (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     name TEXT NOT NULL UNIQUE,
-    created_at DATETIME DEFAULT CURRENT_TIMESTAMP
+    created_at DATETIME DEFAULT CURRENT_TIMESTAMP,
+    deleted_at TEXT DEFAULT NULL
 );
 
 CREATE INDEX IF NOT EXISTS idx_tags_name ON tags(name);
@@ -200,6 +202,9 @@ CREATE TABLE IF NOT EXISTS theses (
     -- CC2r acceptance (collected in student form)
     cc2r BOOLEAN DEFAULT 0,
 
+    -- Soft delete support
+    deleted_at TEXT DEFAULT NULL,
+
     -- Timestamps
     created_at DATETIME DEFAULT CURRENT_TIMESTAMP,
     updated_at DATETIME DEFAULT CURRENT_TIMESTAMP,
@@ -538,11 +543,12 @@ LEFT JOIN authors a ON ta.author_id = a.id
 LEFT JOIN thesis_supervisors ts ON t.id = ts.thesis_id
 LEFT JOIN supervisors s ON ts.supervisor_id = s.id
 LEFT JOIN thesis_languages tl ON t.id = tl.thesis_id
-LEFT JOIN languages l ON tl.language_id = l.id
+LEFT JOIN languages l ON tl.language_id = l.id AND l.deleted_at IS NULL
 LEFT JOIN thesis_formats tf ON t.id = tf.thesis_id
 LEFT JOIN format_types fmt ON tf.format_id = fmt.id
 LEFT JOIN thesis_tags tt ON t.id = tt.thesis_id
-LEFT JOIN tags tg ON tt.tag_id = tg.id
+LEFT JOIN tags tg ON tt.tag_id = tg.id AND tg.deleted_at IS NULL
+WHERE t.deleted_at IS NULL
 GROUP BY t.id;
 
 -- Published theses only (for public view)