install: Handle mount points in rootfs operations

Allow mount points (separate filesystems) to exist during to-filesystem
installations by detecting and skipping them in the empty rootdir check.

When cleaning directories during commit, recursively clean the contents
of mount point directories while preserving the mount point itself. This
is necessary for cases where subdirectories like /var/log or /var/home
are separate logical volumes.

Assisted-by: Claude Code
Signed-off-by: ckyrouac <[email protected]>

Author: ckyrouac

crates/lib/src/install.rs

@@ -1771,6 +1771,19 @@ fn require_empty_rootdir(rootfs_fd: &Dir) -> Result<()> {
         if name == LOST_AND_FOUND {
             continue;
         }
+
+        // Check if this entry is a directory
+        let etype = e.file_type()?;
+        if etype == FileType::dir() {
+            // Check if this directory is a mount point (separate filesystem)
+            // If open_dir_noxdev returns None, it means this directory is on a different device
+            // (i.e., it's a mount point), which is acceptable for to-filesystem installations
+            if rootfs_fd.open_dir_noxdev(&name)?.is_none() {
+                tracing::debug!("Skipping mount point: {name}");
+                continue;
+            }
+        }
+
         // There must be a boot directory (that is empty)
         if name == BOOT {
             let mut entries = rootfs_fd.read_dir(BOOT)?;

crates/ostree-ext/src/commit.rs

@@ -57,10 +57,23 @@ fn clean_subdir(root: &Dir, rootdev: u64) -> Result<()> {
             tracing::trace!("Skipping entry in foreign dev {path:?}");
             continue;
         }
-        // Also ignore bind mounts, if we have a new enough kernel with statx()
-        // that will tell us.
+        // For mount points (e.g., separate LVM volumes under /var), we need to clean
+        // their contents but preserve the directory itself. This is critical for cases
+        // where subdirectories like /var/log or /var/home are separate logical volumes.
         if root.is_mountpoint(&path)?.unwrap_or_default() {
-            tracing::trace!("Skipping mount point {path:?}");
+            if metadata.is_dir() {
+                tracing::debug!("Cleaning contents of mount point directory {path:?}");
+                // Get the device ID of the mountpoint itself
+                let mountpoint_dev = metadata.dev();
+                // Open the mountpoint directory and clean its contents
+                if let Some(mountpoint_dir) = root.open_dir_optional(&path)? {
+                    clean_subdir(&mountpoint_dir, mountpoint_dev)
+                        .with_context(|| format!("Cleaning mountpoint {path:?}"))?;
+                }
+                // Do not remove the directory itself - it's a mount point
+            } else {
+                tracing::trace!("Skipping non-directory mount point {path:?}");
+            }
             continue;
         }
         if metadata.is_dir() {