From 0d42d97e72543a14ccd0843dab9f86497e1de01f Mon Sep 17 00:00:00 2001
From: Pekka Enberg <penberg@turso.tech>
Date: Mon, 22 Dec 2025 15:41:50 +0200
Subject: [PATCH] cli: Fix overlay mount I/O error by unifying whiteout schema
 in SDK

The whiteout table created by `agentfs init --base` was missing the
`parent_path` column that `overlayfs.rs` queries during directory listing.
This caused `get_child_whiteouts()` to fail with a SQL error, which
propagated as an I/O error when running `ls` on the mounted filesystem.

The fix moves the schema definition to a single location in the SDK
(`OverlayFS::init_schema`) to prevent future drift between CLI and SDK.
The CLI now calls this method instead of duplicating the SQL.

Also removes dead `base_type` code that was set but never read.

Fixes #106
---
 cli/src/cmd/init.rs                  | 46 ++++------------------------
 sdk/rust/src/filesystem/overlayfs.rs | 23 ++++++++++----
 2 files changed, 23 insertions(+), 46 deletions(-)

diff --git a/cli/src/cmd/init.rs b/cli/src/cmd/init.rs
index 9efc98f..11a1dfc 100644
--- a/cli/src/cmd/init.rs
+++ b/cli/src/cmd/init.rs
@@ -1,7 +1,7 @@
 use std::path::PathBuf;
 use std::time::{SystemTime, UNIX_EPOCH};
 
-use agentfs_sdk::{agentfs_dir, AgentFS, AgentFSOptions};
+use agentfs_sdk::{agentfs_dir, AgentFS, AgentFSOptions, OverlayFS};
 use anyhow::{Context, Result as AnyhowResult};
 
 pub async fn init_database(
@@ -63,52 +63,18 @@ pub async fn init_database(
         .await
         .context("Failed to initialize database")?;
 
-    // If base is provided, store the overlay configuration
+    // If base is provided, initialize the overlay schema using the SDK
     if let Some(base_path) = base {
-        let conn = agent.get_connection();
-
-        // Create whiteout table for overlay support
-        conn.execute(
-            "CREATE TABLE IF NOT EXISTS fs_whiteout (
-                path TEXT PRIMARY KEY,
-                created_at INTEGER NOT NULL
-            )",
-            (),
-        )
-        .await
-        .context("Failed to create whiteout table")?;
-
-        // Create overlay config table
-        conn.execute(
-            "CREATE TABLE IF NOT EXISTS fs_overlay_config (
-                key TEXT PRIMARY KEY,
-                value TEXT NOT NULL
-            )",
-            (),
-        )
-        .await
-        .context("Failed to create overlay config table")?;
-
-        // Store base path configuration
         let base_path_str = base_path
             .canonicalize()
             .context("Failed to canonicalize base path")?
             .to_string_lossy()
             .to_string();
 
-        conn.execute(
-            "INSERT INTO fs_overlay_config (key, value) VALUES ('base_type', 'hostfs')",
-            (),
-        )
-        .await
-        .context("Failed to store base type")?;
-
-        conn.execute(
-            "INSERT INTO fs_overlay_config (key, value) VALUES ('base_path', ?)",
-            (base_path_str.as_str(),),
-        )
-        .await
-        .context("Failed to store base path")?;
+        // Use SDK's OverlayFS::init_schema to ensure schema consistency
+        OverlayFS::init_schema(&agent.get_connection(), &base_path_str)
+            .await
+            .context("Failed to initialize overlay schema")?;
 
         eprintln!("Created overlay filesystem: {}", db_path.display());
         eprintln!("Agent ID: {}", id);
diff --git a/sdk/rust/src/filesystem/overlayfs.rs b/sdk/rust/src/filesystem/overlayfs.rs
index aadb7cd..a78b017 100644
--- a/sdk/rust/src/filesystem/overlayfs.rs
+++ b/sdk/rust/src/filesystem/overlayfs.rs
@@ -5,7 +5,7 @@ use std::{
     sync::Arc,
     time::{SystemTime, UNIX_EPOCH},
 };
-use turso::Value;
+use turso::{Connection, Value};
 
 use super::{agentfs::AgentFS, DirEntry, FileSystem, FilesystemStats, FsError, Stats};
 
@@ -38,16 +38,15 @@ impl OverlayFS {
         Self { base, delta }
     }
 
-    /// Initialize the overlay filesystem schema (creates whiteout table)
+    /// Initialize the overlay filesystem schema in a database.
     ///
-    /// This must be called before using the overlay filesystem to ensure
-    /// the whiteout tracking table exists in the delta layer.
+    /// This is a static method that can be called without creating an OverlayFS
+    /// instance, useful for CLI tools that need to initialize an overlay database.
     ///
     /// The `base_path` parameter specifies the actual filesystem path that the
     /// base layer represents. This is stored in the delta database so that
     /// tools like `agentfs diff` can determine what files were modified.
-    pub async fn init(&self, base_path: &str) -> Result<()> {
-        let conn = self.delta.get_connection();
+    pub async fn init_schema(conn: &Connection, base_path: &str) -> Result<()> {
         conn.execute(
             "CREATE TABLE IF NOT EXISTS fs_whiteout (
                 path TEXT PRIMARY KEY,
@@ -80,6 +79,18 @@ impl OverlayFS {
         Ok(())
     }
 
+    /// Initialize the overlay filesystem schema (creates whiteout table)
+    ///
+    /// This must be called before using the overlay filesystem to ensure
+    /// the whiteout tracking table exists in the delta layer.
+    ///
+    /// The `base_path` parameter specifies the actual filesystem path that the
+    /// base layer represents. This is stored in the delta database so that
+    /// tools like `agentfs diff` can determine what files were modified.
+    pub async fn init(&self, base_path: &str) -> Result<()> {
+        Self::init_schema(&self.delta.get_connection(), base_path).await
+    }
+
     /// Extract the parent path from a normalized path
     fn parent_path(path: &str) -> String {
         if path == "/" {