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Created January 13, 2026 02:33
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Claude session: 8578009e-f789-47f6-915b-bb85328a99a7
Raw
import.sh
#!/bin/bash
# Import this Claude session: curl -sL <raw_url> | bash
if ! command -v uvx &> /dev/null; then
echo "Installing uv..."
curl -LsSf https://astral.sh/uv/install.sh | sh
export PATH="$HOME/.local/bin:$PATH"
fi
uvx one_claude gist import 62dae992fedee691536317023879c1b1
Raw
session.json
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"title": "noticing msb is missing files in my custom image that I see when I run it with docker. How does it load the oci layers?",
"created_at": "2026-01-08T20:33:25.564000+00:00",
"updated_at": "2026-01-08T20:34:42.256000+00:00"
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"summary": "Fix portal retry loop delay issue #314",
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"content": "noticing msb is missing files in my custom image that I see when I run it with docker. How does it load the oci layers?"
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"thinking": "The user is asking about how microsandbox (msb) loads OCI layers from container images. They're noticing that files are missing when using their custom image with msb compared to when running with Docker directly. This suggests there might be an issue with how layers are being loaded or merged.\n\nLet me explore the codebase to understand how OCI layers are loaded.",
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"prompt": "Find how microsandbox loads OCI image layers. Look for:\n1. How OCI/container images are pulled and extracted\n2. How layers are merged/overlaid to create the final filesystem\n3. Any rootfs or overlay filesystem handling\n4. Look for terms like \"layer\", \"oci\", \"rootfs\", \"overlay\", \"image\", \"manifest\"\n\nThe user is seeing missing files compared to Docker, so focus on the layer extraction and merging logic.",
"description": "Find OCI layer loading code"
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"text": "Perfect! Now I have a complete picture. Let me create a comprehensive summary of my findings.\n\n## Summary\n\nI've successfully analyzed how microsandbox loads and manages OCI image layers. Here are my findings:\n\n---\n\n## OCI Image Layer Loading and Merging in Microsandbox\n\n### 1. **Image Pulling and Layer Extraction**\n\n**Location:** `/home/tato/Desktop/microsandbox/microsandbox-core/lib/oci/registry.rs` and `/home/tato/Desktop/microsandbox/microsandbox-core/lib/management/image.rs`\n\n**How it works:**\n- The `pull_image()` function in `registry.rs` fetches image manifests and configurations from OCI registries\n- For each layer in the manifest, `download_image_blob()` downloads the compressed tar.gz file\n- Downloaded layers are stored in `~/.microsandbox/layers/` directory\n- Layers are identified and stored by their digest (SHA256 hash)\n\n**Key code flow:**\n1. Fetch image manifest and config from registry\n2. For each layer descriptor in manifest:\n - Download blob (compressed tar.gz) with hash verification\n - Save layer to database with digest, media type, and diff_id\n - Link layer to manifest in database\n\n### 2. **Layer Extraction Process**\n\n**Location:** `/home/tato/Desktop/microsandbox/microsandbox-core/lib/management/image.rs`\n\n**Function:** `extract_layer()` and `extract_tar_with_ownership_override()`\n\n**Key features:**\n- Layers are extracted as gzip-compressed tar archives\n- Each layer is extracted to `<digest>.extracted/` subdirectory\n- **Ownership Override:** Original UID/GID/mode from tar entries are stored as xattrs (`user.containers.override_stat`)\n- **Permission Handling:**\n - Files: ensure minimum `u+rw` (0o600)\n - Directories: ensure minimum `u+rwx` (0o700)\n- **Hard Link Processing:** Hard links are collected and created in a second pass after all regular files are extracted\n- Symlinks are preserved as-is without modification\n\n**Potential Issue:** The xattr-based ownership tracking may not fully preserve Docker's semantics if the VM runtime doesn't properly interpret these xattrs.\n\n### 3. **Layer Merging via Overlayfs**\n\n**Location:** `/home/tato/Desktop/microsandbox/microsandbox-core/lib/management/sandbox.rs` and `/home/tato/Desktop/microsandbox/microsandbox-core/lib/vm/vm.rs`\n\n**How layers are stacked:**\n\nIn `setup_image_rootfs()`:\n```\nLayer order (bottom to top):\n1. OCI layer 1 (extracted)\n2. OCI layer 2 (extracted)\n3. ... (more OCI layers)\n4. patch_dir (/.sandbox_scripts and custom config)\n5. top_rw_path (read-write layer for runtime modifications)\n```\n\n**Key code:**\n```rust\n// Get extracted layer paths in order\nlet mut layer_paths = Vec::new();\nfor layer in &layers {\n let layer_path = layers_dir.join(format!(\"{}.{}\", layer.digest, EXTRACTED_LAYER_SUFFIX));\n layer_paths.push(layer_path);\n}\n\n// Add patch and RW layers\nlayer_paths.push(patch_dir); // Contains /.sandbox_scripts and mounts\nlayer_paths.push(top_rw_path); // Read-write overlay for runtime\n\n// Pass to overlayfs\nOk(Rootfs::Overlayfs(layer_paths))\n```\n\n**Passed to libkrun:** In `vm.rs` `apply_config()`:\n```rust\nRootfs::Overlayfs(paths) => {\n let c_paths: Vec<_> = paths\n .iter()\n .map(|p| CString::new(p.to_str().unwrap().as_bytes()).unwrap())\n .collect();\n let c_paths_ptrs = utils::to_null_terminated_c_array(&c_paths);\n unsafe {\n let status = ffi::krun_set_overlayfs_root(ctx_id, c_paths_ptrs.as_ptr());\n }\n}\n```\n\n### 4. **Whiteout and Opaque Marker Support**\n\n**Location:** `/home/tato/Desktop/microsandbox/microsandbox-core/lib/management/rootfs.rs`\n\n**Defined constants:**\n- `OPAQUE_WHITEOUT_MARKER = \".wh..wh..opq\"` - marks directory for complete replacement\n- `WHITEOUT_PREFIX = \".wh.\"` - prefix for files to mark as deleted\n\n**Current Status:** These constants are defined but **NO active processing code found** for handling whiteouts during layer extraction or merging. This is likely delegated to libkrun's overlayfs implementation at runtime.\n\n### 5. **Rootfs Patching**\n\nAfter layer assembly, the sandbox is patched with:\n\n1. **Sandbox Scripts** - `patch_with_sandbox_scripts()`\n - Creates `/.sandbox_scripts/` directory\n - Adds custom scripts with proper shebangs\n - Sets executable permissions (750)\n\n2. **Volume Mounts** - `patch_with_virtiofs_mounts()`\n - Updates `/etc/fstab` with virtiofs mount entries\n - Creates mount point directories\n\n3. **DNS Configuration** - `patch_with_default_dns_settings()`\n - Checks all layers for existing nameservers\n - Adds defaults (1.1.1.1, 8.8.8.8) only if none exist\n\n4. **Stat Override** - `patch_with_stat_override()`\n - Sets `user.containers.override_stat = \"0:0:040755\"` on rootfs\n - Ensures proper directory permissions inside VM\n\n---\n\n## Potential Issue: Missing Files Compared to Docker\n\nThe most likely causes:\n\n1. **Whiteout Files Not Processed:** If Docker removes files using `.wh.*` markers in upper layers, these deletions may not be properly applied if libkrun doesn't interpret the whiteout markers during overlayfs mount setup.\n\n2. **Hard Link Handling:** The current implementation collects hard links and creates them in a second pass. If hard links span layer boundaries or have special permissions, they may not be correctly reconstructed.\n\n3. **Xattr-based Ownership:** Files extracted with modified UID/GID are stored only in xattrs. If the VM runtime or application code doesn't read these xattrs, it may see wrong ownership.\n\n4. **Layer Ordering:** Verify that layers are being assembled in the correct order - later layers should override earlier ones.\n\n5. **File Permissions:** The code forces minimum permissions (0o600 for files, 0o700 for dirs). Docker may preserve exact permissions, which could cause discrepancies.\n\n---\n\n## Key Files for Investigation\n\n1. `/home/tato/Desktop/microsandbox/microsandbox-core/lib/management/image.rs` - Layer extraction\n2. `/home/tato/Desktop/microsandbox/microsandbox-core/lib/management/sandbox.rs` - Layer assembly (lines 536-651)\n3. `/home/tato/Desktop/microsandbox/microsandbox-core/lib/vm/vm.rs` - Overlayfs configuration (lines 330-342)\n4. `/home/tato/Desktop/microsandbox/microsandbox-core/lib/oci/registry.rs` - Image pulling"
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"text": "Perfect! Now I have a complete picture. Let me create a comprehensive summary of my findings.\n\n## Summary\n\nI've successfully analyzed how microsandbox loads and manages OCI image layers. Here are my findings:\n\n---\n\n## OCI Image Layer Loading and Merging in Microsandbox\n\n### 1. **Image Pulling and Layer Extraction**\n\n**Location:** `/home/tato/Desktop/microsandbox/microsandbox-core/lib/oci/registry.rs` and `/home/tato/Desktop/microsandbox/microsandbox-core/lib/management/image.rs`\n\n**How it works:**\n- The `pull_image()` function in `registry.rs` fetches image manifests and configurations from OCI registries\n- For each layer in the manifest, `download_image_blob()` downloads the compressed tar.gz file\n- Downloaded layers are stored in `~/.microsandbox/layers/` directory\n- Layers are identified and stored by their digest (SHA256 hash)\n\n**Key code flow:**\n1. Fetch image manifest and config from registry\n2. For each layer descriptor in manifest:\n - Download blob (compressed tar.gz) with hash verification\n - Save layer to database with digest, media type, and diff_id\n - Link layer to manifest in database\n\n### 2. **Layer Extraction Process**\n\n**Location:** `/home/tato/Desktop/microsandbox/microsandbox-core/lib/management/image.rs`\n\n**Function:** `extract_layer()` and `extract_tar_with_ownership_override()`\n\n**Key features:**\n- Layers are extracted as gzip-compressed tar archives\n- Each layer is extracted to `<digest>.extracted/` subdirectory\n- **Ownership Override:** Original UID/GID/mode from tar entries are stored as xattrs (`user.containers.override_stat`)\n- **Permission Handling:**\n - Files: ensure minimum `u+rw` (0o600)\n - Directories: ensure minimum `u+rwx` (0o700)\n- **Hard Link Processing:** Hard links are collected and created in a second pass after all regular files are extracted\n- Symlinks are preserved as-is without modification\n\n**Potential Issue:** The xattr-based ownership tracking may not fully preserve Docker's semantics if the VM runtime doesn't properly interpret these xattrs.\n\n### 3. **Layer Merging via Overlayfs**\n\n**Location:** `/home/tato/Desktop/microsandbox/microsandbox-core/lib/management/sandbox.rs` and `/home/tato/Desktop/microsandbox/microsandbox-core/lib/vm/vm.rs`\n\n**How layers are stacked:**\n\nIn `setup_image_rootfs()`:\n```\nLayer order (bottom to top):\n1. OCI layer 1 (extracted)\n2. OCI layer 2 (extracted)\n3. ... (more OCI layers)\n4. patch_dir (/.sandbox_scripts and custom config)\n5. top_rw_path (read-write layer for runtime modifications)\n```\n\n**Key code:**\n```rust\n// Get extracted layer paths in order\nlet mut layer_paths = Vec::new();\nfor layer in &layers {\n let layer_path = layers_dir.join(format!(\"{}.{}\", layer.digest, EXTRACTED_LAYER_SUFFIX));\n layer_paths.push(layer_path);\n}\n\n// Add patch and RW layers\nlayer_paths.push(patch_dir); // Contains /.sandbox_scripts and mounts\nlayer_paths.push(top_rw_path); // Read-write overlay for runtime\n\n// Pass to overlayfs\nOk(Rootfs::Overlayfs(layer_paths))\n```\n\n**Passed to libkrun:** In `vm.rs` `apply_config()`:\n```rust\nRootfs::Overlayfs(paths) => {\n let c_paths: Vec<_> = paths\n .iter()\n .map(|p| CString::new(p.to_str().unwrap().as_bytes()).unwrap())\n .collect();\n let c_paths_ptrs = utils::to_null_terminated_c_array(&c_paths);\n unsafe {\n let status = ffi::krun_set_overlayfs_root(ctx_id, c_paths_ptrs.as_ptr());\n }\n}\n```\n\n### 4. **Whiteout and Opaque Marker Support**\n\n**Location:** `/home/tato/Desktop/microsandbox/microsandbox-core/lib/management/rootfs.rs`\n\n**Defined constants:**\n- `OPAQUE_WHITEOUT_MARKER = \".wh..wh..opq\"` - marks directory for complete replacement\n- `WHITEOUT_PREFIX = \".wh.\"` - prefix for files to mark as deleted\n\n**Current Status:** These constants are defined but **NO active processing code found** for handling whiteouts during layer extraction or merging. This is likely delegated to libkrun's overlayfs implementation at runtime.\n\n### 5. **Rootfs Patching**\n\nAfter layer assembly, the sandbox is patched with:\n\n1. **Sandbox Scripts** - `patch_with_sandbox_scripts()`\n - Creates `/.sandbox_scripts/` directory\n - Adds custom scripts with proper shebangs\n - Sets executable permissions (750)\n\n2. **Volume Mounts** - `patch_with_virtiofs_mounts()`\n - Updates `/etc/fstab` with virtiofs mount entries\n - Creates mount point directories\n\n3. **DNS Configuration** - `patch_with_default_dns_settings()`\n - Checks all layers for existing nameservers\n - Adds defaults (1.1.1.1, 8.8.8.8) only if none exist\n\n4. **Stat Override** - `patch_with_stat_override()`\n - Sets `user.containers.override_stat = \"0:0:040755\"` on rootfs\n - Ensures proper directory permissions inside VM\n\n---\n\n## Potential Issue: Missing Files Compared to Docker\n\nThe most likely causes:\n\n1. **Whiteout Files Not Processed:** If Docker removes files using `.wh.*` markers in upper layers, these deletions may not be properly applied if libkrun doesn't interpret the whiteout markers during overlayfs mount setup.\n\n2. **Hard Link Handling:** The current implementation collects hard links and creates them in a second pass. If hard links span layer boundaries or have special permissions, they may not be correctly reconstructed.\n\n3. **Xattr-based Ownership:** Files extracted with modified UID/GID are stored only in xattrs. If the VM runtime or application code doesn't read these xattrs, it may see wrong ownership.\n\n4. **Layer Ordering:** Verify that layers are being assembled in the correct order - later layers should override earlier ones.\n\n5. **File Permissions:** The code forces minimum permissions (0o600 for files, 0o700 for dirs). Docker may preserve exact permissions, which could cause discrepancies.\n\n---\n\n## Key Files for Investigation\n\n1. `/home/tato/Desktop/microsandbox/microsandbox-core/lib/management/image.rs` - Layer extraction\n2. `/home/tato/Desktop/microsandbox/microsandbox-core/lib/management/sandbox.rs` - Layer assembly (lines 536-651)\n3. `/home/tato/Desktop/microsandbox/microsandbox-core/lib/vm/vm.rs` - Overlayfs configuration (lines 330-342)\n4. `/home/tato/Desktop/microsandbox/microsandbox-core/lib/oci/registry.rs` - Image pulling"
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"thinking": "The agent found detailed information about how OCI layers are loaded. The key findings are:\n\n1. Layers are downloaded and extracted to `~/.microsandbox/layers/<digest>.extracted/`\n2. Layers are stacked using overlayfs via libkrun\n3. **Important potential issue**: Whiteout files (`.wh.*` markers) are defined but there's no active processing code found - this is delegated to libkrun\n\nThe most likely cause of missing files is whiteout handling. Let me summarize this for the user.",
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"model": "claude-opus-4-5-20251101",
"id": "msg_01G55Q3DCpp6AzcD5Sz35KKn",
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{
"type": "text",
"text": "Based on my exploration, here's how microsandbox loads OCI layers:\n\n## Layer Loading Flow\n\n1. **Download**: Layers are fetched from registries and saved to `~/.microsandbox/layers/` by digest\n2. **Extract**: Each layer is extracted to `<digest>.extracted/` subdirectory in `image.rs`\n3. **Stack via overlayfs**: Layers are passed to libkrun's `krun_set_overlayfs_root()` in order (bottom to top)\n\n## Most Likely Cause of Missing Files\n\n**Whiteout markers are not being processed during extraction.** The codebase defines:\n- `WHITEOUT_PREFIX = \".wh.\"` - marks files as deleted\n- `OPAQUE_WHITEOUT_MARKER = \".wh..wh..opq\"` - marks directories for complete replacement\n\nBut there's **no active code processing these** during layer extraction. It's delegated to libkrun's overlayfs at runtime.\n\nIf your custom image has upper layers that **delete** files from lower layers using `.wh.*` markers, those deletions may not be applied correctly if libkrun isn't handling them.\n\n## Quick Diagnostic Steps\n\n1. Check if whiteout files exist in your image's extracted layers:\n```bash\nfind ~/.microsandbox/layers -name \".wh.*\" 2>/dev/null\n```\n\n2. Compare extracted layer contents with what Docker shows:\n```bash\n# In msb extracted layers\nls -la ~/.microsandbox/layers/<digest>.extracted/path/to/missing/file\n\n# In Docker\ndocker run --rm your-image ls -la /path/to/missing/file\n```\n\nWould you like me to look at the specific layer extraction code or the libkrun overlayfs integration to identify where the issue might be?"
}
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