fix(fuse): keep the size of a file open for writing across re-listings

B109: an online create seals an empty file on Drive, and until the last
close the written bytes live only in the open handle. A re-listing of
the parent, a size upgrade or a create landing re-interned the node with
Drive's empty size, the kernel capped reads at that size, and SQLite
reported "database disk image is malformed". State::keep_open_write_size
now carries the handle's size and local mtime over in all three places.

The acceptance script waits for My files to mount after a daemon restart
instead of failing at once.

crates/pdfs-fuse/src/drain.rs

@@ -1060,9 +1060,11 @@ impl Core {
             let Some(&ino) = st.by_uid.get(real) else {
                 return;
             };
+            let mut landed = node.clone();
+            st.keep_open_write_size(ino, &mut landed);
             if let Some(e) = st.entries.get_mut(&ino) {
                 e.uid = real.clone();
-                e.node = node.clone();
+                e.node = landed;
             }
             // Where the op said the node goes and where it actually landed can
             // differ — a conflict re-homes it — so the tree follows the parent

crates/pdfs-fuse/src/lib.rs

@@ -2695,6 +2695,10 @@ impl Core {
                     continue;
                 };
                 changed.push(ino);
+                // An open write handle is ahead of the server too (B109).
+                if st.active_writes.contains_key(&ino) {
+                    continue;
+                }
                 let NodeKind::File { claimed_size, .. } = &node.kind else {
                     continue;
                 };

crates/pdfs-fuse/src/state.rs

@@ -800,12 +800,13 @@ impl State {
         self.intern_mem_with_access(parent, node, access)
     }
 
-    fn intern_mem_with_access(&mut self, parent: u64, node: Node, access: Access) -> u64 {
+    fn intern_mem_with_access(&mut self, parent: u64, mut node: Node, access: Access) -> u64 {
         if let Some(&ino) = self.by_uid.get(&node.uid) {
             let changed = self
                 .entries
                 .get(&ino)
                 .is_some_and(|entry| entry.access != access);
+            self.keep_open_write_size(ino, &mut node);
             if let Some(e) = self.entries.get_mut(&ino) {
                 e.node = node;
                 e.parent = parent;
@@ -850,6 +851,23 @@ impl State {
 
     /// Allocate (or reuse) a stable inode for a node that came *from* the
     /// database, which is why nothing is written back.
+    /// Carry the size and mtime of a file open for writing over onto `node`,
+    /// which is about to replace its entry.
+    ///
+    /// The open handle is ahead of anything Drive can report until release
+    /// queues it. Taking the remote's size shrank a SQLite database to its empty
+    /// create while SQLite held it open, and the kernel then capped every read
+    /// at that size (docs/BUGS.md B109).
+    pub(crate) fn keep_open_write_size(&self, ino: u64, node: &mut Node) {
+        let (Some(aw), Some(entry)) = (self.active_writes.get(&ino), self.entries.get(&ino)) else {
+            return;
+        };
+        if let NodeKind::File { claimed_size, .. } = &mut node.kind {
+            *claimed_size = Some(aw.len as i64);
+            node.modification_time = entry.node.modification_time;
+        }
+    }
+
     pub(crate) fn intern_from_db(&mut self, parent: u64, node: Node) -> u64 {
         self.intern_mem(parent, node)
     }
@@ -1900,6 +1918,27 @@ mod tests {
         }
     }
 
+    #[test]
+    fn a_listing_does_not_shrink_a_file_open_for_writing() {
+        let (mut st, _dir) = state();
+        let ino = st.intern(0, node("file", "root", "workload.db", false));
+        let mut h = handle(16384, 0);
+        h.ino = ino;
+        st.active_writes.insert(ino, h);
+        st.set_size(ino, 16384);
+        st.touch_mtime(ino, 500);
+
+        // The remote still holds the empty file the create sealed.
+        st.intern(0, node("file", "root", "workload.db", false));
+        assert_eq!(crate::node_size(&st.entries[&ino].node), 16384);
+        assert_eq!(st.entries[&ino].node.modification_time, 500);
+
+        // Once the handle is gone the remote is authoritative again.
+        st.active_writes.remove(&ino);
+        st.intern(0, node("file", "root", "workload.db", false));
+        assert_eq!(crate::node_size(&st.entries[&ino].node), 0);
+    }
+
     #[test]
     fn a_write_past_the_end_authors_the_hole_it_leaves() {
         // Opened over a 100-byte base, shrunk to 10, then written at 50: bytes

docs/BUGS.md

@@ -12,6 +12,29 @@ Conventions:
 
 ---
 
+## B109 — A re-listing shrinks a file that is open for writing, and SQLite reads it as malformed
+
+**Status:** Fixed (unverified).
+**Found:** 2026-09-29, by the acceptance case "application workloads" on My files. It failed
+several runs in a row with `database disk image is malformed` at the `SELECT COUNT(*)` right
+after a 500-row insert, and the daemon logged nothing. A diagnosis added to the case showed
+`workload.db` at 0 bytes while SQLite still held it open with 16 KiB written.
+
+**Where:** `crates/pdfs-fuse/src/state.rs` (`State::keep_open_write_size`, called from
+`intern_mem_with_access`), the local-uid remap in `crates/pdfs-fuse/src/drain.rs`, and the size
+upgrade in `crates/pdfs-fuse/src/lib.rs`.
+
+**Cause.** An online create seals an empty file on Drive. Until the last close, the written
+bytes live only in the open handle, and the entry's size is the handle's. Any re-listing of the
+parent re-interned the node from Drive, which replaced that size with 0. Such re-listings come
+from event echoes and sibling creates, and SQLite's journal is one. The kernel then got size 0
+from `getattr` and ended SQLite's reads at EOF without asking the daemon, so the database read
+back as empty pages. Queued writes were already protected (B11); open handles were not.
+
+**Fix.** A node that has an open write handle keeps the handle's size and its local mtime when
+a listing, a size upgrade or a create landing replaces its entry. After the last close, the
+queued write takes over as before.
+
 ## B108 — A file deleted during a mirror pass puts the sync folder in `error`
 
 **Status:** Fixed (unverified).
@@ -31,11 +54,6 @@ ended in `error` and logged "item(s) failed; will retry" for files nobody wanted
 does not count as an error. The next pass sees the deletion and handles it like any other.
 Other open failures are still errors.
 
-**Also open from the same run.** "application workloads" on My files failed with
-`database disk image is malformed` at the `SELECT` after the insert. The daemon logged nothing
-for it. The case now reports the step that failed, the database and journal files beside it,
-and which pages differ from a local replay of the same statements.
-
 ## B107 — One read on a stalled connection hangs the reading program for half an hour
 
 **Status:** Fixed (unverified).

docs/CHANGELOG.md

@@ -40,6 +40,9 @@ scratch (user data in `staging/` and `recovery/` is never touched by this).
 - **Editors can save over a file several times in a row.** The fix for B104 could leave the
   upload of a replaced file queued, and the next save onto the same name failed with
   `Input/output error` (B106).
+- **Databases and other files kept open while written no longer read back empty.** When the
+  folder was listed again while a file was still open, its size dropped to what Drive held,
+  often 0 bytes, and SQLite reported `database disk image is malformed` (B109).
 - **Deleting files during a mirror pass no longer marks the folder as failed.** A file removed
   after the pass planned its upload was counted as an error, so the folder showed `error` until
   a later pass (B108).

scripts/fuse-acceptance.py

@@ -3488,9 +3488,17 @@ def run_account(reference: Run, args) -> None:
             "no running pdfs daemon: start proton-drive.service and sign in, "
             "or pass --offline-only for the account-free contract"
         )
+    # A daemon that was just (re)started answers before it has mounted My
+    # files; give it the sync timeout to get there rather than failing at once.
+    deadline = time.monotonic() + timeout
+    while True:
         status = daemon.status()
-    check(bool(status.get("logged_in")), "the daemon is not signed in; run `pdfs login` first")
         mountpoint = (status.get("mount") or {}).get("mountpoint")
+        ready = bool(mountpoint) and is_mountpoint(Path(mountpoint))
+        if ready or not status.get("logged_in") or time.monotonic() >= deadline:
+            break
+        time.sleep(1)
+    check(bool(status.get("logged_in")), "the daemon is not signed in; run `pdfs login` first")
     check(
         bool(mountpoint) and is_mountpoint(Path(mountpoint)),
         f"My files is not mounted (daemon reports {mountpoint!r})",