Merge branch 'main' into cal/fix-content-rows-issues

fix: boris rev
feat: content lock
2026-07-31 21:26:40 +00:00 · 2026-07-23 20:58:46 +01:00 · 2026-07-22 18:09:52 +01:00 · 2026-07-22 18:00:49 +01:00 · 2026-07-22 17:24:24 +01:00 · 2026-07-22 17:23:37 +01:00
21 changed files with 915 additions and 292 deletions
@@ -0,0 +1,74 @@
+{
+  "db_name": "SQLite",
+  "query": "\n\t\tINSERT INTO instance_files (\n\t\t\tid,\n\t\t\tinstance_id,\n\t\t\trelative_path,\n\t\t\tfile_name,\n\t\t\tenabled,\n\t\t\tsha1,\n\t\t\tsize,\n\t\t\tmissing,\n\t\t\tadded_at,\n\t\t\tmodified_at\n\t\t)\n\t\tVALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n\t\tON CONFLICT (instance_id, relative_path) DO UPDATE SET\n\t\t\tfile_name = excluded.file_name,\n\t\t\tenabled = excluded.enabled,\n\t\t\tsha1 = excluded.sha1,\n\t\t\tsize = excluded.size,\n\t\t\tmissing = excluded.missing,\n\t\t\tmodified_at = excluded.modified_at\n\t\tRETURNING\n\t\t\tid,\n\t\t\tinstance_id,\n\t\t\trelative_path,\n\t\t\tfile_name,\n\t\t\tenabled,\n\t\t\tsha1,\n\t\t\tsize,\n\t\t\tmissing,\n\t\t\tadded_at,\n\t\t\tmodified_at\n\t\t",
+  "describe": {
+    "columns": [
+      {
+        "name": "id",
+        "ordinal": 0,
+        "type_info": "Text"
+      },
+      {
+        "name": "instance_id",
+        "ordinal": 1,
+        "type_info": "Text"
+      },
+      {
+        "name": "relative_path",
+        "ordinal": 2,
+        "type_info": "Text"
+      },
+      {
+        "name": "file_name",
+        "ordinal": 3,
+        "type_info": "Text"
+      },
+      {
+        "name": "enabled",
+        "ordinal": 4,
+        "type_info": "Integer"
+      },
+      {
+        "name": "sha1",
+        "ordinal": 5,
+        "type_info": "Text"
+      },
+      {
+        "name": "size",
+        "ordinal": 6,
+        "type_info": "Integer"
+      },
+      {
+        "name": "missing",
+        "ordinal": 7,
+        "type_info": "Integer"
+      },
+      {
+        "name": "added_at",
+        "ordinal": 8,
+        "type_info": "Integer"
+      },
+      {
+        "name": "modified_at",
+        "ordinal": 9,
+        "type_info": "Integer"
+      }
+    ],
+    "parameters": {
+      "Right": 10
+    },
+    "nullable": [
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false
+    ]
+  },
+  "hash": "59a314ee065e24af6d7138fcf11eed0eafc29732a15f25d051964660941c8d33"
+}
@@ -1,20 +0,0 @@
-{
-  "db_name": "SQLite",
-  "query": "\n\t\t\tSELECT id\n\t\t\tFROM instance_content_entries\n\t\t\tWHERE content_set_id = ?\n\t\t\t\tAND project_id = ?\n\t\t\t\tAND version_id = ?\n\t\t\tORDER BY modified_at DESC\n\t\t\tLIMIT 1\n\t\t\t",
-  "describe": {
-    "columns": [
-      {
-        "name": "id",
-        "ordinal": 0,
-        "type_info": "Text"
-      }
-    ],
-    "parameters": {
-      "Right": 3
-    },
-    "nullable": [
-      false
-    ]
-  },
-  "hash": "636bb0c426ac275d64f7c84b3349894d10faf920d56814c0c2336e4cd5002743"
-}
@@ -0,0 +1,92 @@
+{
+  "db_name": "SQLite",
+  "query": "\n\t\t\tINSERT INTO instance_content_entries (\n\t\t\t\tid,\n\t\t\t\tinstance_id,\n\t\t\t\tcontent_set_id,\n\t\t\t\tfile_id,\n\t\t\t\tproject_type,\n\t\t\t\tproject_id,\n\t\t\t\tversion_id,\n\t\t\t\tsource_kind,\n\t\t\t\tserver_requirement,\n\t\t\t\tclient_requirement,\n\t\t\t\tenabled,\n\t\t\t\tadded_at,\n\t\t\t\tmodified_at\n\t\t\t)\n\t\t\tVALUES (?, ?, ?, NULL, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n\t\t\tRETURNING\n\t\t\t\tid,\n\t\t\t\tinstance_id,\n\t\t\t\tcontent_set_id,\n\t\t\t\tfile_id,\n\t\t\t\tproject_type,\n\t\t\t\tproject_id,\n\t\t\t\tversion_id,\n\t\t\t\tsource_kind,\n\t\t\t\tserver_requirement,\n\t\t\t\tclient_requirement,\n\t\t\t\tenabled,\n\t\t\t\tadded_at,\n\t\t\t\tmodified_at\n\t\t\t",
+  "describe": {
+    "columns": [
+      {
+        "name": "id",
+        "ordinal": 0,
+        "type_info": "Text"
+      },
+      {
+        "name": "instance_id",
+        "ordinal": 1,
+        "type_info": "Text"
+      },
+      {
+        "name": "content_set_id",
+        "ordinal": 2,
+        "type_info": "Text"
+      },
+      {
+        "name": "file_id",
+        "ordinal": 3,
+        "type_info": "Text"
+      },
+      {
+        "name": "project_type",
+        "ordinal": 4,
+        "type_info": "Text"
+      },
+      {
+        "name": "project_id",
+        "ordinal": 5,
+        "type_info": "Text"
+      },
+      {
+        "name": "version_id",
+        "ordinal": 6,
+        "type_info": "Text"
+      },
+      {
+        "name": "source_kind",
+        "ordinal": 7,
+        "type_info": "Text"
+      },
+      {
+        "name": "server_requirement",
+        "ordinal": 8,
+        "type_info": "Text"
+      },
+      {
+        "name": "client_requirement",
+        "ordinal": 9,
+        "type_info": "Text"
+      },
+      {
+        "name": "enabled",
+        "ordinal": 10,
+        "type_info": "Integer"
+      },
+      {
+        "name": "added_at",
+        "ordinal": 11,
+        "type_info": "Integer"
+      },
+      {
+        "name": "modified_at",
+        "ordinal": 12,
+        "type_info": "Integer"
+      }
+    ],
+    "parameters": {
+      "Right": 12
+    },
+    "nullable": [
+      false,
+      false,
+      false,
+      true,
+      false,
+      true,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false
+    ]
+  },
+  "hash": "6a4dd5b455a6aa19bb866faa915b8bfd4b7aca017e919d6240d7e1e2fc412e5c"
+}
@@ -1,20 +0,0 @@
-{
-  "db_name": "SQLite",
-  "query": "\n\t\t\tSELECT id\n\t\t\tFROM instance_content_entries\n\t\t\tWHERE content_set_id = ? AND file_id = ?\n\t\t\tORDER BY modified_at DESC\n\t\t\tLIMIT 1\n\t\t\t",
-  "describe": {
-    "columns": [
-      {
-        "name": "id",
-        "ordinal": 0,
-        "type_info": "Text"
-      }
-    ],
-    "parameters": {
-      "Right": 2
-    },
-    "nullable": [
-      false
-    ]
-  },
-  "hash": "6a6e05b5c64a7061046383f69e07bc3f24cbde279858f3f440a78089b696a718"
-}
@@ -0,0 +1,74 @@
+{
+  "db_name": "SQLite",
+  "query": "\n\t\tUPDATE instance_files\n\t\tSET\n\t\t\tmissing = ?,\n\t\t\tmodified_at = ?\n\t\tWHERE id = ?\n\t\tRETURNING\n\t\t\tid,\n\t\t\tinstance_id,\n\t\t\trelative_path,\n\t\t\tfile_name,\n\t\t\tenabled,\n\t\t\tsha1,\n\t\t\tsize,\n\t\t\tmissing,\n\t\t\tadded_at,\n\t\t\tmodified_at\n\t\t",
+  "describe": {
+    "columns": [
+      {
+        "name": "id",
+        "ordinal": 0,
+        "type_info": "Text"
+      },
+      {
+        "name": "instance_id",
+        "ordinal": 1,
+        "type_info": "Text"
+      },
+      {
+        "name": "relative_path",
+        "ordinal": 2,
+        "type_info": "Text"
+      },
+      {
+        "name": "file_name",
+        "ordinal": 3,
+        "type_info": "Text"
+      },
+      {
+        "name": "enabled",
+        "ordinal": 4,
+        "type_info": "Integer"
+      },
+      {
+        "name": "sha1",
+        "ordinal": 5,
+        "type_info": "Text"
+      },
+      {
+        "name": "size",
+        "ordinal": 6,
+        "type_info": "Integer"
+      },
+      {
+        "name": "missing",
+        "ordinal": 7,
+        "type_info": "Integer"
+      },
+      {
+        "name": "added_at",
+        "ordinal": 8,
+        "type_info": "Integer"
+      },
+      {
+        "name": "modified_at",
+        "ordinal": 9,
+        "type_info": "Integer"
+      }
+    ],
+    "parameters": {
+      "Right": 3
+    },
+    "nullable": [
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false
+    ]
+  },
+  "hash": "6d76a6f26705044500983aaae9796a39ac667278b0c805da2320384a37c3baa1"
+}
@@ -1,12 +0,0 @@
-{
-  "db_name": "SQLite",
-  "query": "\n\t\tINSERT INTO instance_content_entries (\n\t\t\tid,\n\t\t\tinstance_id,\n\t\t\tcontent_set_id,\n\t\t\tfile_id,\n\t\t\tproject_type,\n\t\t\tproject_id,\n\t\t\tversion_id,\n\t\t\tsource_kind,\n\t\t\tserver_requirement,\n\t\t\tclient_requirement,\n\t\t\tenabled,\n\t\t\tadded_at,\n\t\t\tmodified_at\n\t\t)\n\t\tVALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n\t\tON CONFLICT(id) DO UPDATE SET\n\t\t\tfile_id = excluded.file_id,\n\t\t\tproject_type = excluded.project_type,\n\t\t\tproject_id = excluded.project_id,\n\t\t\tversion_id = excluded.version_id,\n\t\t\tsource_kind = excluded.source_kind,\n\t\t\tserver_requirement = excluded.server_requirement,\n\t\t\tclient_requirement = excluded.client_requirement,\n\t\t\tenabled = excluded.enabled,\n\t\t\tmodified_at = excluded.modified_at\n\t\t",
-  "describe": {
-    "columns": [],
-    "parameters": {
-      "Right": 13
-    },
-    "nullable": []
-  },
-  "hash": "81e6135eeba87a5f2084e0747b4675ff87456469e98c07520023981e3b3d121a"
-}
@@ -1,12 +0,0 @@
-{
-  "db_name": "SQLite",
-  "query": "\n\t\tUPDATE instance_files\n\t\tSET\n\t\t\tmissing = 1,\n\t\t\tmodified_at = ?\n\t\tWHERE instance_id = ?\n\t\t",
-  "describe": {
-    "columns": [],
-    "parameters": {
-      "Right": 2
-    },
-    "nullable": []
-  },
-  "hash": "8c54b73c00cfc43b47ca08cca4dbdc381afa80c2f493d04c8a54875619386caf"
-}
@@ -0,0 +1,92 @@
+{
+  "db_name": "SQLite",
+  "query": "\n\t\t\tINSERT INTO instance_content_entries (\n\t\t\t\tid,\n\t\t\t\tinstance_id,\n\t\t\t\tcontent_set_id,\n\t\t\t\tfile_id,\n\t\t\t\tproject_type,\n\t\t\t\tproject_id,\n\t\t\t\tversion_id,\n\t\t\t\tsource_kind,\n\t\t\t\tserver_requirement,\n\t\t\t\tclient_requirement,\n\t\t\t\tenabled,\n\t\t\t\tadded_at,\n\t\t\t\tmodified_at\n\t\t\t)\n\t\t\tVALUES (?, ?, ?, NULL, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n\t\t\tON CONFLICT (content_set_id, project_id, version_id)\n\t\t\t\tWHERE file_id IS NULL\n\t\t\t\t\tAND project_id IS NOT NULL\n\t\t\t\t\tAND version_id IS NOT NULL\n\t\t\tDO UPDATE SET\n\t\t\t\tinstance_id = excluded.instance_id,\n\t\t\t\tproject_type = excluded.project_type,\n\t\t\t\tsource_kind = excluded.source_kind,\n\t\t\t\tserver_requirement = excluded.server_requirement,\n\t\t\t\tclient_requirement = excluded.client_requirement,\n\t\t\t\tenabled = excluded.enabled,\n\t\t\t\tmodified_at = excluded.modified_at\n\t\t\tRETURNING\n\t\t\t\tid,\n\t\t\t\tinstance_id,\n\t\t\t\tcontent_set_id,\n\t\t\t\tfile_id,\n\t\t\t\tproject_type,\n\t\t\t\tproject_id,\n\t\t\t\tversion_id,\n\t\t\t\tsource_kind,\n\t\t\t\tserver_requirement,\n\t\t\t\tclient_requirement,\n\t\t\t\tenabled,\n\t\t\t\tadded_at,\n\t\t\t\tmodified_at\n\t\t\t",
+  "describe": {
+    "columns": [
+      {
+        "name": "id",
+        "ordinal": 0,
+        "type_info": "Text"
+      },
+      {
+        "name": "instance_id",
+        "ordinal": 1,
+        "type_info": "Text"
+      },
+      {
+        "name": "content_set_id",
+        "ordinal": 2,
+        "type_info": "Text"
+      },
+      {
+        "name": "file_id",
+        "ordinal": 3,
+        "type_info": "Text"
+      },
+      {
+        "name": "project_type",
+        "ordinal": 4,
+        "type_info": "Text"
+      },
+      {
+        "name": "project_id",
+        "ordinal": 5,
+        "type_info": "Text"
+      },
+      {
+        "name": "version_id",
+        "ordinal": 6,
+        "type_info": "Text"
+      },
+      {
+        "name": "source_kind",
+        "ordinal": 7,
+        "type_info": "Text"
+      },
+      {
+        "name": "server_requirement",
+        "ordinal": 8,
+        "type_info": "Text"
+      },
+      {
+        "name": "client_requirement",
+        "ordinal": 9,
+        "type_info": "Text"
+      },
+      {
+        "name": "enabled",
+        "ordinal": 10,
+        "type_info": "Integer"
+      },
+      {
+        "name": "added_at",
+        "ordinal": 11,
+        "type_info": "Integer"
+      },
+      {
+        "name": "modified_at",
+        "ordinal": 12,
+        "type_info": "Integer"
+      }
+    ],
+    "parameters": {
+      "Right": 12
+    },
+    "nullable": [
+      false,
+      false,
+      false,
+      true,
+      false,
+      true,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false
+    ]
+  },
+  "hash": "8daa2109fa7affe35b94d1fe3823ffe7601c0bca00db4ea0c8dc709bcf5642eb"
+}
@@ -1,12 +0,0 @@
-{
-  "db_name": "SQLite",
-  "query": "\n\t\tINSERT INTO instance_files (\n\t\t\tid,\n\t\t\tinstance_id,\n\t\t\trelative_path,\n\t\t\tfile_name,\n\t\t\tenabled,\n\t\t\tsha1,\n\t\t\tsize,\n\t\t\tmissing,\n\t\t\tadded_at,\n\t\t\tmodified_at\n\t\t)\n\t\tVALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n\t\tON CONFLICT (instance_id, relative_path) DO UPDATE SET\n\t\t\tfile_name = excluded.file_name,\n\t\t\tenabled = excluded.enabled,\n\t\t\tsha1 = excluded.sha1,\n\t\t\tsize = excluded.size,\n\t\t\tmissing = excluded.missing,\n\t\t\tmodified_at = excluded.modified_at\n\t\t",
-  "describe": {
-    "columns": [],
-    "parameters": {
-      "Right": 10
-    },
-    "nullable": []
-  },
-  "hash": "aabe81dce68b38d0e5a9748da0df4f0f982f22861d13a848b09538b3ef594847"
-}
@@ -0,0 +1,92 @@
+{
+  "db_name": "SQLite",
+  "query": "\n\t\t\tINSERT INTO instance_content_entries (\n\t\t\t\tid,\n\t\t\t\tinstance_id,\n\t\t\t\tcontent_set_id,\n\t\t\t\tfile_id,\n\t\t\t\tproject_type,\n\t\t\t\tproject_id,\n\t\t\t\tversion_id,\n\t\t\t\tsource_kind,\n\t\t\t\tserver_requirement,\n\t\t\t\tclient_requirement,\n\t\t\t\tenabled,\n\t\t\t\tadded_at,\n\t\t\t\tmodified_at\n\t\t\t)\n\t\t\tVALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n\t\t\tON CONFLICT (content_set_id, file_id)\n\t\t\t\tWHERE file_id IS NOT NULL\n\t\t\tDO UPDATE SET\n\t\t\t\tinstance_id = excluded.instance_id,\n\t\t\t\tproject_type = excluded.project_type,\n\t\t\t\tproject_id = excluded.project_id,\n\t\t\t\tversion_id = excluded.version_id,\n\t\t\t\tsource_kind = excluded.source_kind,\n\t\t\t\tserver_requirement = excluded.server_requirement,\n\t\t\t\tclient_requirement = excluded.client_requirement,\n\t\t\t\tenabled = excluded.enabled,\n\t\t\t\tmodified_at = excluded.modified_at\n\t\t\tRETURNING\n\t\t\t\tid,\n\t\t\t\tinstance_id,\n\t\t\t\tcontent_set_id,\n\t\t\t\tfile_id,\n\t\t\t\tproject_type,\n\t\t\t\tproject_id,\n\t\t\t\tversion_id,\n\t\t\t\tsource_kind,\n\t\t\t\tserver_requirement,\n\t\t\t\tclient_requirement,\n\t\t\t\tenabled,\n\t\t\t\tadded_at,\n\t\t\t\tmodified_at\n\t\t\t",
+  "describe": {
+    "columns": [
+      {
+        "name": "id",
+        "ordinal": 0,
+        "type_info": "Text"
+      },
+      {
+        "name": "instance_id",
+        "ordinal": 1,
+        "type_info": "Text"
+      },
+      {
+        "name": "content_set_id",
+        "ordinal": 2,
+        "type_info": "Text"
+      },
+      {
+        "name": "file_id",
+        "ordinal": 3,
+        "type_info": "Text"
+      },
+      {
+        "name": "project_type",
+        "ordinal": 4,
+        "type_info": "Text"
+      },
+      {
+        "name": "project_id",
+        "ordinal": 5,
+        "type_info": "Text"
+      },
+      {
+        "name": "version_id",
+        "ordinal": 6,
+        "type_info": "Text"
+      },
+      {
+        "name": "source_kind",
+        "ordinal": 7,
+        "type_info": "Text"
+      },
+      {
+        "name": "server_requirement",
+        "ordinal": 8,
+        "type_info": "Text"
+      },
+      {
+        "name": "client_requirement",
+        "ordinal": 9,
+        "type_info": "Text"
+      },
+      {
+        "name": "enabled",
+        "ordinal": 10,
+        "type_info": "Integer"
+      },
+      {
+        "name": "added_at",
+        "ordinal": 11,
+        "type_info": "Integer"
+      },
+      {
+        "name": "modified_at",
+        "ordinal": 12,
+        "type_info": "Integer"
+      }
+    ],
+    "parameters": {
+      "Right": 13
+    },
+    "nullable": [
+      false,
+      false,
+      false,
+      true,
+      false,
+      true,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false,
+      false
+    ]
+  },
+  "hash": "fbdf27acfedbf52fe79ef2db7cf29b5cd8b86308ef1202b3f06570bbb6e1419e"
+}
@@ -0,0 +1,46 @@
+-- Older app versions could save the same content entry more than once. Remove the older copies before preventing future duplicates.
+WITH ranked_entries AS (
+	SELECT
+		id,
+		ROW_NUMBER() OVER (
+			PARTITION BY content_set_id, file_id
+			ORDER BY modified_at DESC, added_at DESC, id DESC
+		) AS duplicate_rank
+	FROM instance_content_entries
+	WHERE file_id IS NOT NULL
+)
+DELETE FROM instance_content_entries
+WHERE id IN (
+	SELECT id
+	FROM ranked_entries
+	WHERE duplicate_rank > 1
+);
+
+WITH ranked_entries AS (
+	SELECT
+		id,
+		ROW_NUMBER() OVER (
+			PARTITION BY content_set_id, project_id, version_id
+			ORDER BY modified_at DESC, added_at DESC, id DESC
+		) AS duplicate_rank
+	FROM instance_content_entries
+	WHERE file_id IS NULL
+		AND project_id IS NOT NULL
+		AND version_id IS NOT NULL
+)
+DELETE FROM instance_content_entries
+WHERE id IN (
+	SELECT id
+	FROM ranked_entries
+	WHERE duplicate_rank > 1
+);
+
+CREATE UNIQUE INDEX instance_content_entries_content_set_file_unique
+	ON instance_content_entries(content_set_id, file_id)
+	WHERE file_id IS NOT NULL;
+
+CREATE UNIQUE INDEX instance_content_entries_content_set_project_version_unique
+	ON instance_content_entries(content_set_id, project_id, version_id)
+	WHERE file_id IS NULL
+		AND project_id IS NOT NULL
+		AND version_id IS NOT NULL;
@@ -798,6 +798,16 @@ pub(crate) async fn install_zipped_mrpack_files_with_reporter(
                let downloaded_bytes = file.len() as u64;

                let path = target_path;
+				content_context
+					.reporter
+					.preserve_failure_context(
+						context.clone(),
+						write(&path, &file, &state.io_semaphore).await,
+					)
+					.await?;
+				let modified_at_ns = crate::state::file_modified_at_ns(
+					&io::metadata(&path).await?,
+				)?;

                {
                    let _permit = state.install_db_semaphore.acquire().await?;
@@ -809,6 +819,7 @@ pub(crate) async fn install_zipped_mrpack_files_with_reporter(
                                file.clone(),
                                &content_context.instance_path,
                                project.path.as_str(),
+								modified_at_ns,
                                project
                                    .hashes
                                    .get(&PackFileHash::Sha1)
@@ -822,14 +833,6 @@ pub(crate) async fn install_zipped_mrpack_files_with_reporter(
                        .await?;
                }

-                content_context
-                    .reporter
-                    .preserve_failure_context(
-                        context.clone(),
-                        write(&path, &file, &state.io_semaphore).await,
-                    )
-                    .await?;
-
                if let Some(project_type) =
                    ProjectType::get_from_parent_folder(project.path.as_str())
                {
@@ -998,6 +1001,8 @@ pub(crate) async fn install_zipped_mrpack_files_with_reporter(
        let (size, hash) = reporter
            .preserve_failure_context(override_context, extract_result)
            .await?;
+        let modified_at_ns =
+            crate::state::file_modified_at_ns(&io::metadata(&path).await?)?;

        {
            let _permit = state.install_db_semaphore.acquire().await?;
@@ -1016,6 +1021,7 @@ pub(crate) async fn install_zipped_mrpack_files_with_reporter(
                        &instance_path,
                        relative_override_file_path.as_str(),
                        size,
+                        modified_at_ns,
                        hash.clone(),
                        ProjectType::get_from_parent_folder(
                            relative_override_file_path.as_str(),
@@ -785,6 +785,7 @@ async fn remove_existing_imported_pack_content(
    metadata: &crate::state::InstanceMetadata,
    state: &State,
 ) -> crate::Result<()> {
+    let _content_lock = state.lock_instance_content(instance_id).await;
    let entries = content_rows::get_content_entries(
        &metadata.applied_content_set.id,
        &state.pool,
@@ -821,18 +822,20 @@ async fn remove_existing_imported_pack_content(
            continue;
        };
        crate::util::io::remove_file(base.join(&file.relative_path)).await?;
+        let mut tx = state.pool.begin().await?;
        content_rows::remove_content_entries_for_file(
            &metadata.applied_content_set.id,
            &file.id,
-            &state.pool,
+            &mut tx,
        )
        .await?;
        content_rows::remove_instance_file_by_relative_path(
            instance_id,
            &file.relative_path,
-            &state.pool,
+            &mut tx,
        )
        .await?;
+        tx.commit().await?;
    }

    Ok(())
@@ -373,6 +373,8 @@ impl<'de> serde::Deserialize<'de> for CachedFileUpdate {
 pub struct CachedFileHash {
    pub path: String,
    pub size: u64,
+    #[serde(default)]
+    pub modified_at_ns: u64,
    pub hash: String,
    pub project_type: Option<ProjectType>,
    #[serde(default)]
@@ -387,6 +389,37 @@ pub struct KnownModrinthFile<'a> {
    pub version_id: &'a str,
 }

+pub(crate) fn file_modified_at_ns(
+    metadata: &std::fs::Metadata,
+) -> std::io::Result<u64> {
+    let elapsed = metadata
+        .modified()?
+        .duration_since(std::time::UNIX_EPOCH)
+        .map_err(std::io::Error::other)?;
+
+    Ok(elapsed
+        .as_secs()
+        .saturating_mul(1_000_000_000)
+        .saturating_add(u64::from(elapsed.subsec_nanos())))
+}
+
+pub(crate) fn file_hash_cache_key(
+    size: u64,
+    modified_at_ns: u64,
+    path: &str,
+) -> String {
+    format!("v2-{size}-{modified_at_ns}-{path}")
+}
+
+fn file_hash_path_from_cache_key(key: &str) -> Option<&str> {
+    let mut parts = key.splitn(4, '-');
+    (parts.next()? == "v2").then_some(())?;
+    parts.next()?.parse::<u64>().ok()?;
+    parts.next()?.parse::<u64>().ok()?;
+    let path = parts.next()?;
+    (!path.is_empty()).then_some(path)
+}
+
 #[derive(Serialize, Deserialize, Clone, Debug)]
 pub struct CachedLoaderManifest {
    pub loader: String,
@@ -674,13 +707,11 @@ impl CacheValue {
            | CacheValue::GameVersions(_)
            | CacheValue::DonationPlatforms(_) => DEFAULT_ID.to_string(),

-            CacheValue::FileHash(hash) => {
-                format!(
-                    "{}-{}",
-                    hash.size,
-                    hash.path.trim_end_matches(".disabled")
-                )
-            }
+            CacheValue::FileHash(hash) => file_hash_cache_key(
+                hash.size,
+                hash.modified_at_ns,
+                hash.path.trim_end_matches(".disabled"),
+            ),
            CacheValue::FileUpdate(hash) => {
                format!(
                    "{}-{}-{}-{}",
@@ -1518,13 +1549,20 @@ impl CachedEntry {
                    instances_dir: &Path,
                    key: String,
                ) -> crate::Result<(CachedEntry, bool)> {
-                    let path =
-                        key.split_once('-').map(|x| x.1).unwrap_or_default();
+                    let path = file_hash_path_from_cache_key(&key).ok_or_else(
+                        || {
+                            crate::ErrorKind::InputError(format!(
+                                "Invalid file hash cache key: {key}",
+                            ))
+                        },
+                    )?;

                    let full_path = instances_dir.join(path);

                    let mut file = tokio::fs::File::open(&full_path).await?;
-                    let size = file.metadata().await?.len();
+                    let metadata = file.metadata().await?;
+                    let size = metadata.len();
+                    let modified_at_ns = file_modified_at_ns(&metadata)?;

                    let mut hasher = sha1_smol::Sha1::new();

@@ -1544,6 +1582,7 @@ impl CachedEntry {
                        CacheValue::FileHash(CachedFileHash {
                            path: path.to_string(),
                            size,
+                            modified_at_ns,
                            hash,
                            project_type: ProjectType::get_from_parent_folder(
                                &full_path,
@@ -2139,6 +2178,7 @@ pub async fn cache_file_hash(
    bytes: bytes::Bytes,
    instance_id: &str,
    path: &str,
+    modified_at_ns: u64,
    known_hash: Option<&str>,
    project_type: Option<ProjectType>,
    known_modrinth_file: Option<KnownModrinthFile<'_>>,
@@ -2156,6 +2196,7 @@ pub async fn cache_file_hash(
        instance_id,
        path,
        size as u64,
+        modified_at_ns,
        hash,
        project_type,
        known_modrinth_file,
@@ -2168,6 +2209,7 @@ pub async fn cache_file_hash_metadata(
    instance_id: &str,
    path: &str,
    size: u64,
+    modified_at_ns: u64,
    hash: String,
    project_type: Option<ProjectType>,
    known_modrinth_file: Option<KnownModrinthFile<'_>>,
@@ -2186,6 +2228,7 @@ pub async fn cache_file_hash_metadata(
        &[CacheValue::FileHash(CachedFileHash {
            path: format!("{instance_id}/{path}"),
            size,
+            modified_at_ns,
            hash,
            project_type,
            project_id,
@@ -1,4 +1,4 @@
-use crate::state::ProjectType;
+use crate::state::{ProjectType, file_hash_cache_key, file_modified_at_ns};
 use crate::util::io::{self, IOError};
 use std::path::{Path, PathBuf};

@@ -44,17 +44,23 @@ pub(crate) fn scan_content_files(
                continue;
            }

-            let size = path.metadata().map_err(IOError::from)?.len();
+            let metadata = path.metadata().map_err(IOError::from)?;
+            let size = metadata.len();
+            let modified_at_ns =
+                file_modified_at_ns(&metadata).map_err(IOError::from)?;
            let relative_path = format!("{folder}/{file_name}");
+            let hash_cache_key = file_hash_cache_key(
+                size,
+                modified_at_ns,
+                &format!("{instance_path}/{relative_path}"),
+            );

            files.push(ScannedContentFile {
                relative_path,
                file_name: file_name.to_string(),
                enabled: !file_name.ends_with(".disabled"),
                size,
-                hash_cache_key: format!(
-                    "{size}-{instance_path}/{folder}/{file_name}"
-                ),
+                hash_cache_key,
            });
        }
    }
@@ -419,33 +419,47 @@ where
    rows.into_iter().map(TryInto::try_into).collect()
 }

-pub(crate) async fn mark_instance_files_missing(
-    instance_id: &str,
+pub(crate) async fn set_instance_file_missing(
+    file_id: &str,
+    missing: bool,
    tx: &mut Transaction<'_, Sqlite>,
-) -> crate::Result<()> {
+) -> crate::Result<Option<InstanceFile>> {
+    let missing = i64::from(missing);
    let modified_at = Utc::now().timestamp();
-
-    sqlx::query!(
+    let row = sqlx::query_as!(
+        InstanceFileRow,
        "
 		UPDATE instance_files
 		SET
-			missing = 1,
+			missing = ?,
 			modified_at = ?
-		WHERE instance_id = ?
+		WHERE id = ?
+		RETURNING
+			id,
+			instance_id,
+			relative_path,
+			file_name,
+			enabled,
+			sha1,
+			size,
+			missing,
+			added_at,
+			modified_at
 		",
+        missing,
        modified_at,
-        instance_id,
+        file_id,
    )
-    .execute(&mut **tx)
+    .fetch_optional(&mut **tx)
    .await?;

-    Ok(())
+    row.map(TryInto::try_into).transpose()
 }

 pub(crate) async fn upsert_instance_file(
    file: &InstanceFile,
    tx: &mut Transaction<'_, Sqlite>,
-) -> crate::Result<()> {
+) -> crate::Result<InstanceFile> {
    let id = file.id.as_str();
    let instance_id = file.instance_id.as_str();
    let relative_path = file.relative_path.as_str();
@@ -457,7 +471,8 @@ pub(crate) async fn upsert_instance_file(
    let added_at = file.added_at.timestamp();
    let modified_at = file.modified_at.timestamp();

-    sqlx::query!(
+    let row = sqlx::query_as!(
+        InstanceFileRow,
        "
 		INSERT INTO instance_files (
 			id,
@@ -479,6 +494,17 @@ pub(crate) async fn upsert_instance_file(
 			size = excluded.size,
 			missing = excluded.missing,
 			modified_at = excluded.modified_at
+		RETURNING
+			id,
+			instance_id,
+			relative_path,
+			file_name,
+			enabled,
+			sha1,
+			size,
+			missing,
+			added_at,
+			modified_at
 		",
        id,
        instance_id,
@@ -491,10 +517,10 @@ pub(crate) async fn upsert_instance_file(
        added_at,
        modified_at,
    )
-    .execute(&mut **tx)
+    .fetch_one(&mut **tx)
    .await?;

-    Ok(())
+    row.try_into()
 }

 pub(crate) async fn get_content_entries<'e, E>(
@@ -575,19 +601,11 @@ pub(crate) async fn get_instance_file_by_relative_path(

 pub(crate) async fn upsert_instance_file_from_parts(
    input: UpsertInstanceFile<'_>,
-    pool: &SqlitePool,
+    tx: &mut Transaction<'_, Sqlite>,
 ) -> crate::Result<InstanceFile> {
-    let existing = get_instance_file_by_relative_path(
-        input.instance_id,
-        input.relative_path,
-        pool,
-    )
-    .await?;
+    let now = Utc::now();
    let file = InstanceFile {
-        id: existing
-            .as_ref()
-            .map(|file| file.id.clone())
-            .unwrap_or_else(|| format!("instance-file:{}", Uuid::new_v4())),
+        id: format!("instance-file:{}", Uuid::new_v4()),
        instance_id: input.instance_id.to_string(),
        relative_path: input.relative_path.to_string(),
        file_name: input.file_name.to_string(),
@@ -595,18 +613,11 @@ pub(crate) async fn upsert_instance_file_from_parts(
        sha1: input.sha1.to_string(),
        size: input.size,
        missing: input.missing,
-        added_at: existing
-            .as_ref()
-            .map(|file| file.added_at)
-            .unwrap_or_else(Utc::now),
-        modified_at: Utc::now(),
+        added_at: now,
+        modified_at: now,
    };

-    let mut tx = pool.begin().await?;
-    upsert_instance_file(&file, &mut tx).await?;
-    tx.commit().await?;
-
-    Ok(file)
+    upsert_instance_file(&file, tx).await
 }

 pub(crate) async fn rename_instance_file(
@@ -615,11 +626,10 @@ pub(crate) async fn rename_instance_file(
    new_relative_path: &str,
    new_file_name: &str,
    enabled: bool,
-    pool: &SqlitePool,
+    tx: &mut Transaction<'_, Sqlite>,
 ) -> crate::Result<Option<InstanceFile>> {
    let enabled = i64::from(enabled);
    let modified_at = Utc::now().timestamp();
-    let mut tx = pool.begin().await?;

    let source_id = sqlx::query_scalar!(
        "
@@ -630,7 +640,7 @@ pub(crate) async fn rename_instance_file(
        instance_id,
        old_relative_path,
    )
-    .fetch_optional(&mut *tx)
+    .fetch_optional(&mut **tx)
    .await?;
    let target_id = sqlx::query_scalar!(
        "
@@ -641,7 +651,7 @@ pub(crate) async fn rename_instance_file(
        instance_id,
        new_relative_path,
    )
-    .fetch_optional(&mut *tx)
+    .fetch_optional(&mut **tx)
    .await?;

    if let (Some(source_id), Some(target_id)) =
@@ -669,7 +679,7 @@ pub(crate) async fn rename_instance_file(
            target_id,
            source_id,
        )
-        .execute(&mut *tx)
+        .execute(&mut **tx)
        .await?;

        sqlx::query!(
@@ -683,7 +693,7 @@ pub(crate) async fn rename_instance_file(
            instance_id,
            target_id,
        )
-        .execute(&mut *tx)
+        .execute(&mut **tx)
        .await?;

        sqlx::query!(
@@ -693,7 +703,7 @@ pub(crate) async fn rename_instance_file(
 				",
            target_id,
        )
-        .execute(&mut *tx)
+        .execute(&mut **tx)
        .await?;
    }

@@ -715,19 +725,29 @@ pub(crate) async fn rename_instance_file(
        instance_id,
        old_relative_path,
    )
-    .execute(&mut *tx)
+    .execute(&mut **tx)
    .await?;

-    tx.commit().await?;
+    let row = sqlx::query_as!(
+        InstanceFileRow,
+        "
+		SELECT *
+		FROM instance_files
+		WHERE instance_id = ? AND relative_path = ?
+		",
+        instance_id,
+        new_relative_path,
+    )
+    .fetch_optional(&mut **tx)
+    .await?;

-    get_instance_file_by_relative_path(instance_id, new_relative_path, pool)
-        .await
+    row.map(TryInto::try_into).transpose()
 }

 pub(crate) async fn remove_instance_file_by_relative_path(
    instance_id: &str,
    relative_path: &str,
-    pool: &SqlitePool,
+    tx: &mut Transaction<'_, Sqlite>,
 ) -> crate::Result<()> {
    sqlx::query!(
        "
@@ -737,7 +757,7 @@ pub(crate) async fn remove_instance_file_by_relative_path(
        instance_id,
        relative_path,
    )
-    .execute(pool)
+    .execute(&mut **tx)
    .await?;

    Ok(())
@@ -800,142 +820,202 @@ pub(crate) async fn get_content_entry_by_file(

 pub(crate) async fn upsert_content_entry_from_parts(
    input: UpsertContentEntry<'_>,
-    pool: &SqlitePool,
+    tx: &mut Transaction<'_, Sqlite>,
 ) -> crate::Result<ContentEntry> {
-    let existing_id = if let Some(file_id) = input.file_id {
-        sqlx::query_scalar!(
+    let id = format!("content-entry:{}", Uuid::new_v4());
+    let project_type = input.project_type.get_name();
+    let source_kind = input.source_kind.as_str();
+    let server_requirement = input.server_requirement.as_str();
+    let client_requirement = input.client_requirement.as_str();
+    let enabled = i64::from(input.enabled);
+    let now = Utc::now().timestamp();
+    let row = if let Some(file_id) = input.file_id {
+        sqlx::query_as!(
+            ContentEntryRow,
            "
-			SELECT id
-			FROM instance_content_entries
-			WHERE content_set_id = ? AND file_id = ?
-			ORDER BY modified_at DESC
-			LIMIT 1
+			INSERT INTO instance_content_entries (
+				id,
+				instance_id,
+				content_set_id,
+				file_id,
+				project_type,
+				project_id,
+				version_id,
+				source_kind,
+				server_requirement,
+				client_requirement,
+				enabled,
+				added_at,
+				modified_at
+			)
+			VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+			ON CONFLICT (content_set_id, file_id)
+				WHERE file_id IS NOT NULL
+			DO UPDATE SET
+				instance_id = excluded.instance_id,
+				project_type = excluded.project_type,
+				project_id = excluded.project_id,
+				version_id = excluded.version_id,
+				source_kind = excluded.source_kind,
+				server_requirement = excluded.server_requirement,
+				client_requirement = excluded.client_requirement,
+				enabled = excluded.enabled,
+				modified_at = excluded.modified_at
+			RETURNING
+				id,
+				instance_id,
+				content_set_id,
+				file_id,
+				project_type,
+				project_id,
+				version_id,
+				source_kind,
+				server_requirement,
+				client_requirement,
+				enabled,
+				added_at,
+				modified_at
 			",
+            id,
+            input.instance_id,
            input.content_set_id,
            file_id,
+            project_type,
+            input.project_id,
+            input.version_id,
+            source_kind,
+            server_requirement,
+            client_requirement,
+            enabled,
+            now,
+            now,
        )
-        .fetch_optional(pool)
+        .fetch_one(&mut **tx)
        .await?
    } else if let (Some(project_id), Some(version_id)) =
        (input.project_id, input.version_id)
    {
-        sqlx::query_scalar!(
+        sqlx::query_as!(
+            ContentEntryRow,
            "
-			SELECT id
-			FROM instance_content_entries
-			WHERE content_set_id = ?
-				AND project_id = ?
-				AND version_id = ?
-			ORDER BY modified_at DESC
-			LIMIT 1
+			INSERT INTO instance_content_entries (
+				id,
+				instance_id,
+				content_set_id,
+				file_id,
+				project_type,
+				project_id,
+				version_id,
+				source_kind,
+				server_requirement,
+				client_requirement,
+				enabled,
+				added_at,
+				modified_at
+			)
+			VALUES (?, ?, ?, NULL, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+			ON CONFLICT (content_set_id, project_id, version_id)
+				WHERE file_id IS NULL
+					AND project_id IS NOT NULL
+					AND version_id IS NOT NULL
+			DO UPDATE SET
+				instance_id = excluded.instance_id,
+				project_type = excluded.project_type,
+				source_kind = excluded.source_kind,
+				server_requirement = excluded.server_requirement,
+				client_requirement = excluded.client_requirement,
+				enabled = excluded.enabled,
+				modified_at = excluded.modified_at
+			RETURNING
+				id,
+				instance_id,
+				content_set_id,
+				file_id,
+				project_type,
+				project_id,
+				version_id,
+				source_kind,
+				server_requirement,
+				client_requirement,
+				enabled,
+				added_at,
+				modified_at
 			",
+            id,
+            input.instance_id,
            input.content_set_id,
+            project_type,
            project_id,
            version_id,
+            source_kind,
+            server_requirement,
+            client_requirement,
+            enabled,
+            now,
+            now,
        )
-        .fetch_optional(pool)
+        .fetch_one(&mut **tx)
        .await?
    } else {
-        None
-    };
-    let now = Utc::now();
-    let entry = ContentEntry {
-        id: existing_id
-            .unwrap_or_else(|| format!("content-entry:{}", Uuid::new_v4())),
-        instance_id: input.instance_id.to_string(),
-        content_set_id: input.content_set_id.to_string(),
-        file_id: input.file_id.map(ToString::to_string),
-        project_type: input.project_type,
-        project_id: input.project_id.map(ToString::to_string),
-        version_id: input.version_id.map(ToString::to_string),
-        source_kind: input.source_kind,
-        server_requirement: input.server_requirement,
-        client_requirement: input.client_requirement,
-        enabled: input.enabled,
-        added_at: now,
-        modified_at: now,
+        sqlx::query_as!(
+            ContentEntryRow,
+            "
+			INSERT INTO instance_content_entries (
+				id,
+				instance_id,
+				content_set_id,
+				file_id,
+				project_type,
+				project_id,
+				version_id,
+				source_kind,
+				server_requirement,
+				client_requirement,
+				enabled,
+				added_at,
+				modified_at
+			)
+			VALUES (?, ?, ?, NULL, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+			RETURNING
+				id,
+				instance_id,
+				content_set_id,
+				file_id,
+				project_type,
+				project_id,
+				version_id,
+				source_kind,
+				server_requirement,
+				client_requirement,
+				enabled,
+				added_at,
+				modified_at
+			",
+            id,
+            input.instance_id,
+            input.content_set_id,
+            project_type,
+            input.project_id,
+            input.version_id,
+            source_kind,
+            server_requirement,
+            client_requirement,
+            enabled,
+            now,
+            now,
+        )
+        .fetch_one(&mut **tx)
+        .await?
    };

-    let added_at = get_content_entry_by_id(&entry.id, pool)
-        .await?
-        .map(|entry| entry.added_at)
-        .unwrap_or(entry.added_at);
-    let id = entry.id.as_str();
-    let entry_instance_id = entry.instance_id.as_str();
-    let content_set_id = entry.content_set_id.as_str();
-    let file_id = entry.file_id.as_deref();
-    let project_type = entry.project_type.get_name();
-    let project_id = entry.project_id.as_deref();
-    let version_id = entry.version_id.as_deref();
-    let source_kind = entry.source_kind.as_str();
-    let server_requirement = entry.server_requirement.as_str();
-    let client_requirement = entry.client_requirement.as_str();
-    let enabled = i64::from(entry.enabled);
-    let added_at = added_at.timestamp();
-    let modified_at = entry.modified_at.timestamp();
-
-    sqlx::query!(
-        "
-		INSERT INTO instance_content_entries (
-			id,
-			instance_id,
-			content_set_id,
-			file_id,
-			project_type,
-			project_id,
-			version_id,
-			source_kind,
-			server_requirement,
-			client_requirement,
-			enabled,
-			added_at,
-			modified_at
-		)
-		VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
-		ON CONFLICT(id) DO UPDATE SET
-			file_id = excluded.file_id,
-			project_type = excluded.project_type,
-			project_id = excluded.project_id,
-			version_id = excluded.version_id,
-			source_kind = excluded.source_kind,
-			server_requirement = excluded.server_requirement,
-			client_requirement = excluded.client_requirement,
-			enabled = excluded.enabled,
-			modified_at = excluded.modified_at
-		",
-        id,
-        entry_instance_id,
-        content_set_id,
-        file_id,
-        project_type,
-        project_id,
-        version_id,
-        source_kind,
-        server_requirement,
-        client_requirement,
-        enabled,
-        added_at,
-        modified_at,
-    )
-    .execute(pool)
-    .await?;
-
-    get_content_entry_by_id(&entry.id, pool)
-        .await?
-        .ok_or_else(|| {
-            crate::ErrorKind::OtherError(format!(
-                "Failed to read content entry {} after upsert",
-                entry.id
-            ))
-            .into()
-        })
+    row.try_into()
 }

 pub(crate) async fn set_content_entry_enabled_for_file(
    content_set_id: &str,
    file_id: &str,
    enabled: bool,
-    pool: &SqlitePool,
+    tx: &mut Transaction<'_, Sqlite>,
 ) -> crate::Result<bool> {
    let enabled = i64::from(enabled);
    let modified_at = Utc::now().timestamp();
@@ -951,7 +1031,7 @@ pub(crate) async fn set_content_entry_enabled_for_file(
        content_set_id,
        file_id,
    )
-    .execute(pool)
+    .execute(&mut **tx)
    .await?;

    Ok(result.rows_affected() > 0)
@@ -960,7 +1040,7 @@ pub(crate) async fn set_content_entry_enabled_for_file(
 pub(crate) async fn remove_content_entries_for_file(
    content_set_id: &str,
    file_id: &str,
-    pool: &SqlitePool,
+    tx: &mut Transaction<'_, Sqlite>,
 ) -> crate::Result<()> {
    sqlx::query!(
        "
@@ -970,7 +1050,7 @@ pub(crate) async fn remove_content_entries_for_file(
        content_set_id,
        file_id,
    )
-    .execute(pool)
+    .execute(&mut **tx)
    .await?;

    Ok(())
@@ -502,6 +502,7 @@ pub(crate) async fn add_project_bytes(
    version_id: Option<&str>,
    state: &State,
 ) -> crate::Result<String> {
+    let _content_lock = state.lock_instance_content(instance_id).await;
    let scope = resolve_content_scope(instance_id, None, state).await?;
    let project_type = match project_type {
        Some(project_type) => project_type,
@@ -515,10 +516,14 @@ pub(crate) async fn add_project_bytes(
        None => fetch::sha1_async(bytes.clone()).await?,
    };

+    fetch::write(&full_path, &bytes, &state.io_semaphore).await?;
+    let modified_at_ns =
+        crate::state::file_modified_at_ns(&io::metadata(&full_path).await?)?;
    cache_file_hash(
        bytes.clone(),
        &scope.instance.id,
        &relative_path,
+        modified_at_ns,
        Some(&sha1),
        Some(project_type),
        project_id.zip(version_id).map(|(project_id, version_id)| {
@@ -530,8 +535,8 @@ pub(crate) async fn add_project_bytes(
        &state.pool,
    )
    .await?;
-    fetch::write(&full_path, &bytes, &state.io_semaphore).await?;

+    let mut tx = state.pool.begin().await?;
    let file = content_rows::upsert_instance_file_from_parts(
        content_rows::UpsertInstanceFile {
            instance_id: &scope.instance.id,
@@ -542,7 +547,7 @@ pub(crate) async fn add_project_bytes(
            size: bytes.len() as u64,
            missing: false,
        },
-        &state.pool,
+        &mut tx,
    )
    .await?;
    upsert_entry_for_file(
@@ -552,9 +557,10 @@ pub(crate) async fn add_project_bytes(
        project_id,
        version_id,
        source_kind,
-        &state.pool,
+        &mut tx,
    )
    .await?;
+    tx.commit().await?;

    Ok(relative_path)
 }
@@ -570,12 +576,14 @@ pub(crate) async fn record_project_file(
    version_id: Option<&str>,
    state: &State,
 ) -> crate::Result<()> {
+    let _content_lock = state.lock_instance_content(instance_id).await;
    let scope = resolve_content_scope(instance_id, None, state).await?;
    let file_name = Path::new(relative_path)
        .file_name()
        .unwrap_or_default()
        .to_string_lossy()
        .to_string();
+    let mut tx = state.pool.begin().await?;
    let file = content_rows::upsert_instance_file_from_parts(
        content_rows::UpsertInstanceFile {
            instance_id: &scope.instance.id,
@@ -586,7 +594,7 @@ pub(crate) async fn record_project_file(
            size,
            missing: false,
        },
-        &state.pool,
+        &mut tx,
    )
    .await?;
    upsert_entry_for_file(
@@ -596,9 +604,12 @@ pub(crate) async fn record_project_file(
        project_id,
        version_id,
        source_kind,
-        &state.pool,
+        &mut tx,
    )
-    .await
+    .await?;
+    tx.commit().await?;
+
+    Ok(())
 }

 pub(crate) async fn toggle_disable_project(
@@ -607,6 +618,7 @@ pub(crate) async fn toggle_disable_project(
    desired_enabled: Option<bool>,
    state: &State,
 ) -> crate::Result<String> {
+    let _content_lock = state.lock_instance_content(instance_id).await;
    let scope = resolve_content_scope(instance_id, None, state).await?;
    let base = instance_full_path(state, &scope.instance);
    let trimmed = project_path.trim_end_matches(".disabled");
@@ -640,13 +652,14 @@ pub(crate) async fn toggle_disable_project(
        .unwrap_or_default()
        .to_string_lossy()
        .to_string();
+    let mut tx = state.pool.begin().await?;
    let file = match content_rows::rename_instance_file(
        &scope.instance.id,
        &current_path,
        &new_path,
        &file_name,
        enabled,
-        &state.pool,
+        &mut tx,
    )
    .await?
    {
@@ -658,21 +671,24 @@ pub(crate) async fn toggle_disable_project(
                &new_path,
                &file_name,
                enabled,
-                &state.pool,
+                &mut tx,
            )
            .await?
            {
                Some(file) => file,
-                None => index_existing_file(&scope, &new_path, state).await?,
+                None => {
+                    index_existing_file(&scope, &new_path, state, &mut tx)
+                        .await?
+                }
            }
        }
-        None => index_existing_file(&scope, &new_path, state).await?,
+        None => index_existing_file(&scope, &new_path, state, &mut tx).await?,
    };
    let updated_entry = content_rows::set_content_entry_enabled_for_file(
        &scope.content_set_id,
        &file.id,
        enabled,
-        &state.pool,
+        &mut tx,
    )
    .await?;
    if !updated_entry {
@@ -689,10 +705,11 @@ pub(crate) async fn toggle_disable_project(
            None,
            None,
            ContentSourceKind::Local,
-            &state.pool,
+            &mut tx,
        )
        .await?;
    }
+    tx.commit().await?;

    Ok(new_path)
 }
@@ -702,6 +719,7 @@ pub(crate) async fn remove_project(
    project_path: &str,
    state: &State,
 ) -> crate::Result<()> {
+    let _content_lock = state.lock_instance_content(instance_id).await;
    let scope = resolve_content_scope(instance_id, None, state).await?;
    let base = instance_full_path(state, &scope.instance);
    let file = content_rows::get_instance_file_by_relative_path(
@@ -718,18 +736,20 @@ pub(crate) async fn remove_project(
    }

    if let Some(file) = file {
+        let mut tx = state.pool.begin().await?;
        content_rows::remove_content_entries_for_file(
            &scope.content_set_id,
            &file.id,
-            &state.pool,
+            &mut tx,
        )
        .await?;
        content_rows::remove_instance_file_by_relative_path(
            &scope.instance.id,
            project_path,
-            &state.pool,
+            &mut tx,
        )
        .await?;
+        tx.commit().await?;
    }

    Ok(())
@@ -810,6 +830,7 @@ async fn index_existing_file(
    scope: &ContentScope,
    relative_path: &str,
    state: &State,
+    tx: &mut sqlx::Transaction<'_, sqlx::Sqlite>,
 ) -> crate::Result<InstanceFile> {
    let full_path =
        instance_full_path(state, &scope.instance).join(relative_path);
@@ -836,7 +857,7 @@ async fn index_existing_file(
            size,
            missing: false,
        },
-        &state.pool,
+        tx,
    )
    .await?;
    upsert_entry_for_file(
@@ -846,7 +867,7 @@ async fn index_existing_file(
        None,
        None,
        ContentSourceKind::Local,
-        &state.pool,
+        tx,
    )
    .await?;

@@ -860,7 +881,7 @@ async fn upsert_entry_for_file(
    project_id: Option<&str>,
    version_id: Option<&str>,
    source_kind: ContentSourceKind,
-    pool: &sqlx::SqlitePool,
+    tx: &mut sqlx::Transaction<'_, sqlx::Sqlite>,
 ) -> crate::Result<()> {
    content_rows::upsert_content_entry_from_parts(
        content_rows::UpsertContentEntry {
@@ -875,7 +896,7 @@ async fn upsert_entry_for_file(
            client_requirement: ContentRequirement::Required,
            enabled: file.enabled,
        },
-        pool,
+        tx,
    )
    .await?;

@@ -11,8 +11,9 @@ pub(crate) async fn remove_instance(
        .ok_or_else(|| {
            crate::ErrorKind::InputError("Unknown instance".to_string())
        })?;
+    let _content_lock = state.lock_instance_content(instance_id).await;

-    instance_rows::delete_instance_by_id(&instance.id, &state.pool).await?;
+    delete_instance_row_and_content_lock(&instance.id, state).await?;

    let path = state.directories.instances_dir().join(&instance.path);
    if path.exists() {
@@ -21,3 +22,14 @@ pub(crate) async fn remove_instance(

    Ok(())
 }
+
+async fn delete_instance_row_and_content_lock(
+    instance_id: &str,
+    state: &State,
+) -> crate::Result<()> {
+    // Keep these together so deleted instances cannot leave stale entries in the per-instance lock map.
+    instance_rows::delete_instance_by_id(instance_id, &state.pool).await?;
+    state.remove_instance_content_lock(instance_id);
+
+    Ok(())
+}
@@ -1,9 +1,9 @@
 use crate::State;
 use crate::state::instances::adapters::{filesystem, sqlite};
 use crate::state::instances::{Instance, InstanceFile};
-use crate::state::{CachedEntry, ProjectType};
+use crate::state::{CachedEntry, ProjectType, file_hash_cache_key};
 use chrono::Utc;
-use std::collections::HashMap;
+use std::collections::{HashMap, HashSet};
 use uuid::Uuid;

 pub(crate) async fn sync_content_files(
@@ -24,6 +24,7 @@ pub(crate) async fn sync_instance_content_files(
    instance: &Instance,
    state: &State,
 ) -> crate::Result<Vec<InstanceFile>> {
+    let _content_lock = state.lock_instance_content(&instance.id).await;
    let scanned = filesystem::scan_content_files(
        &state.directories.instances_dir(),
        &instance.path,
@@ -43,10 +44,10 @@ pub(crate) async fn sync_instance_content_files(
        .into_iter()
        .map(|hash| {
            (
-                format!(
-                    "{}-{}",
+                file_hash_cache_key(
                    hash.size,
-                    hash.path.trim_end_matches(".disabled")
+                    hash.modified_at_ns,
+                    hash.path.trim_end_matches(".disabled"),
                ),
                hash,
            )
@@ -55,6 +56,17 @@ pub(crate) async fn sync_instance_content_files(
    let existing_files =
        sqlite::content_rows::get_instance_files(&instance.id, &state.pool)
            .await?;
+    let scanned_paths = scanned
+        .iter()
+        .map(|file| file.relative_path.clone())
+        .collect::<HashSet<_>>();
+    let missing_file_ids = existing_files
+        .iter()
+        .filter(|file| {
+            !file.missing && !scanned_paths.contains(&file.relative_path)
+        })
+        .map(|file| file.id.clone())
+        .collect::<Vec<_>>();
    let existing_files_by_path = existing_files
        .into_iter()
        .map(|file| (file.relative_path.clone(), file))
@@ -62,13 +74,17 @@ pub(crate) async fn sync_instance_content_files(

    let now = Utc::now();
    let mut files = Vec::new();
+    let mut present_without_hash_ids = Vec::new();

    for file in scanned {
        let hash_key = file.hash_cache_key.trim_end_matches(".disabled");
+        let existing_file = existing_files_by_path.get(&file.relative_path);
        let Some(hash) = hashes_by_key.get(hash_key) else {
+            if let Some(existing_file) = existing_file {
+                present_without_hash_ids.push(existing_file.id.clone());
+            }
            continue;
        };
-        let existing_file = existing_files_by_path.get(&file.relative_path);

        files.push(InstanceFile {
            id: existing_file
@@ -87,16 +103,33 @@ pub(crate) async fn sync_instance_content_files(
    }

    let mut tx = state.pool.begin().await?;
-    sqlite::content_rows::mark_instance_files_missing(&instance.id, &mut tx)
+    for file_id in missing_file_ids {
+        sqlite::content_rows::set_instance_file_missing(
+            &file_id, true, &mut tx,
+        )
        .await?;
+    }

+    let mut stored_files =
+        Vec::with_capacity(files.len() + present_without_hash_ids.len());
+    for file_id in present_without_hash_ids {
+        if let Some(file) = sqlite::content_rows::set_instance_file_missing(
+            &file_id, false, &mut tx,
+        )
+        .await?
+        {
+            stored_files.push(file);
+        }
+    }
    for file in &files {
-        sqlite::content_rows::upsert_instance_file(file, &mut tx).await?;
+        stored_files.push(
+            sqlite::content_rows::upsert_instance_file(file, &mut tx).await?,
+        );
    }

    tx.commit().await?;

-    Ok(files)
+    Ok(stored_files)
 }

 pub(crate) fn project_type_for_file(
@@ -213,7 +213,10 @@ where
                            .find(|x| x.hashes.get("sha512") == Some(&sha512))
                        && let Some(sha1) = file.hashes.get("sha1")
                    {
-                        if let Ok(metadata) = full_path.metadata() {
+                        if let Ok(metadata) = full_path.metadata()
+                            && let Ok(modified_at_ns) =
+                                state::file_modified_at_ns(&metadata)
+                        {
                            let file_name = format!(
                                "{}/{}",
                                profile.path,
@@ -225,6 +228,7 @@ where
                                CachedFileHash {
                                    path: file_name,
                                    size: metadata.len(),
+                                    modified_at_ns,
                                    hash: sha1.clone(),
                                    project_type:
                                        ProjectType::get_from_parent_folder(
@@ -1,8 +1,9 @@
 //! Theseus state management system
 use crate::util::fetch::{FetchSemaphore, IoSemaphore};
+use dashmap::DashMap;
 use std::sync::Arc;
 use std::sync::atomic::AtomicBool;
-use tokio::sync::{OnceCell, Semaphore};
+use tokio::sync::{Mutex, OnceCell, OwnedMutexGuard, Semaphore};

 use crate::state::instances::watcher::FileWatcher;
 use sqlx::SqlitePool;
@@ -71,6 +72,8 @@ pub struct State {
    pub api_semaphore: FetchSemaphore,
    pub(crate) install_job_semaphore: Semaphore,
    pub(crate) install_db_semaphore: Semaphore,
+    /// Serializes filesystem reconciliation and content mutations per instance.
+    instance_content_locks: DashMap<String, Arc<Mutex<()>>>,

    /// Discord RPC
    pub discord_rpc: DiscordGuard,
@@ -95,6 +98,23 @@ pub struct State {
 }

 impl State {
+    pub(crate) async fn lock_instance_content(
+        &self,
+        instance_id: &str,
+    ) -> OwnedMutexGuard<()> {
+        let lock = self
+            .instance_content_locks
+            .entry(instance_id.to_string())
+            .or_insert_with(|| Arc::new(Mutex::new(())))
+            .clone();
+
+        lock.lock_owned().await
+    }
+
+    pub(crate) fn remove_instance_content_lock(&self, instance_id: &str) {
+        let _ = self.instance_content_locks.remove(instance_id);
+    }
+
    pub async fn init(app_identifier: String) -> crate::Result<()> {
        let state = LAUNCHER_STATE
            .get_or_try_init(move || Self::initialize_state(app_identifier))
@@ -210,6 +230,7 @@ impl State {
            api_semaphore,
            install_job_semaphore: Semaphore::new(MAX_CONCURRENT_INSTALL_JOBS),
            install_db_semaphore: Semaphore::new(1),
+            instance_content_locks: DashMap::new(),
            discord_rpc,
            process_manager,
            friends_socket,
Author	SHA1	Message	Date
Calum H.andGitHub	2066fab7d5	Merge branch 'main' into cal/fix-content-rows-issues	2026-07-23 20:58:46 +01:00
Calum H. (IMB11)	e26b6c4bda	fix: boris rev	2026-07-22 18:09:52 +01:00
Calum H. (IMB11)	467a868adc	feat: content lock	2026-07-22 18:00:49 +01:00
Calum H. (IMB11)	3c31864299	fix: invalidate cached hashes for modified files	2026-07-22 17:24:24 +01:00
Calum H. (IMB11)	d2e3b7cd92	fix: make file and content entry writes atomic	2026-07-22 17:23:37 +01:00
Calum H. (IMB11)	f53b062707	fix: prevent duplicate content entries	2026-07-22 17:21:46 +01:00
Calum H. (IMB11)	1cb24e78af	fix: serialize per-instance content mutations	2026-07-22 17:20:10 +01:00
Calum H. (IMB11)	6a02995c48	fix: preserve present files when hashing fails	2026-07-22 17:19:29 +01:00
Calum H. (IMB11)	d19ec795c9	fix: preserve instance file identity during upsert	2026-07-22 17:17:49 +01:00