Added youki build and fromatting of scripts

Replace inline boot testing with standalone runit.sh runner for clarity:
- Remove scripts/lib/testing.sh source and boot_tests stage from build.sh
- Remove --skip-tests option from build.sh and rebuild-after-zinit.sh
- Update all docs to reference runit.sh for QEMU/cloud-hypervisor testing
- Add comprehensive claude.md as AI assistant entry point with guidelines

Testing is now fully decoupled from build pipeline; use ./runit.sh for
QEMU/cloud-hypervisor validation after builds complete.

Dockerfile

@@ -20,6 +20,7 @@ RUN apk add --no-cache \
     musl-utils \
     pkgconfig \
     openssl openssl-dev \
+    libseccomp libseccomp-dev \
     perl \
     shadow \
     bash \

README.md

@@ -103,8 +103,7 @@ zosbuilder/
 │   │   ├── alpine.sh       # Alpine operations
 │   │   ├── components.sh   # source building
 │   │   ├── initramfs.sh    # assembly & optimization
-│   │   ├── kernel.sh       # kernel building
+│   │   └── kernel.sh       # kernel building
-│   │   └── testing.sh      # QEMU/cloud-hypervisor
 │   ├── build.sh            # main orchestrator
 │   └── clean.sh            # cleanup script
 ├── initramfs/              # build output (generated)
@@ -244,34 +243,40 @@ Services are migrated from existing `configs/zinit/` directory with proper initi
 ### Phase 6: Packaging
 1. Create `initramfs.cpio.xz` with XZ compression
 2. Build kernel with embedded initramfs
-3. Generate `vmlinuz.efi`
+3. Generate `vmlinuz.efi` (default kernel)
+4. Generate versioned kernel: `vmlinuz-{VERSION}-{ZINIT_HASH}.efi`
+5. Optionally upload versioned kernel to S3 (set `UPLOAD_KERNEL=true`)
 
 ## Testing
 
 ### QEMU Testing
 ```bash
-# Boot test with QEMU
+# Boot test with QEMU (default)
-./scripts/test.sh --qemu
+./runit.sh
 
-# With serial console
+# With custom parameters
-./scripts/test.sh --qemu --serial
+./runit.sh --hypervisor qemu --memory 2048 --disks 3
 ```
 
 ### cloud-hypervisor Testing
 ```bash
 # Boot test with cloud-hypervisor
-./scripts/test.sh --cloud-hypervisor
+./runit.sh --hypervisor ch
+
+# With disk reset
+./runit.sh --hypervisor ch --reset --disks 5
 ```
 
-### Custom Testing
+### Advanced Options
 ```bash
-# Manual QEMU command
+# See all options
-qemu-system-x86_64 \
+./runit.sh --help
-  -kernel dist/vmlinuz.efi \
+
-  -m 512M \
+# Custom disk size and bridge
-  -nographic \
+./runit.sh --disk-size 20G --bridge zosbr --disks 4
-  -serial mon:stdio \
+
-  -append "console=ttyS0,115200 console=tty1 loglevel=7"
+# Environment variables
+HYPERVISOR=ch NUM_DISKS=5 ./runit.sh
 ```
 
 ## Size Optimization
@@ -321,7 +326,7 @@ jobs:
     - name: Build
       run: ./scripts/build.sh
     - name: Test
-      run: ./scripts/test.sh --qemu
+      run: ./runit.sh --hypervisor qemu
 ```
 
 ## Advanced Usage
@@ -354,6 +359,72 @@ function build_myapp() {
 }
 ```
 
+### S3 Uploads (Kernel & RFS Flists)
+
+Automatically upload build artifacts to S3-compatible storage:
+
+#### Configuration
+
+Create `config/rfs.conf`:
+
+```bash
+S3_ENDPOINT="https://s3.example.com:9000"
+S3_REGION="us-east-1"
+S3_BUCKET="zos"
+S3_PREFIX="flists/zosbuilder"
+S3_ACCESS_KEY="YOUR_ACCESS_KEY"
+S3_SECRET_KEY="YOUR_SECRET_KEY"
+```
+
+#### Upload Kernel
+
+```bash
+# Enable kernel upload
+UPLOAD_KERNEL=true ./scripts/build.sh
+
+# Custom kernel subpath (default: kernel)
+KERNEL_SUBPATH=kernels UPLOAD_KERNEL=true ./scripts/build.sh
+```
+
+**Uploaded files:**
+- `s3://{bucket}/{prefix}/kernel/vmlinuz-{VERSION}-{ZINIT_HASH}.efi` - Versioned kernel
+- `s3://{bucket}/{prefix}/kernel/kernels.txt` - Text index (one kernel per line)
+- `s3://{bucket}/{prefix}/kernel/kernels.json` - JSON index with metadata
+
+**Index files:**
+The build automatically generates and uploads index files listing all available kernels in the S3 bucket. This enables:
+- Easy kernel selection in web UIs (dropdown menus)
+- Programmatic access without S3 API listing
+- Metadata like upload timestamp and kernel count (JSON format)
+
+**JSON index format:**
+```json
+{
+  "kernels": [
+    "vmlinuz-6.12.44-Zero-OS-abc1234.efi",
+    "vmlinuz-6.12.44-Zero-OS-def5678.efi"
+  ],
+  "updated": "2025-01-04T12:00:00Z",
+  "count": 2
+}
+```
+
+#### Upload RFS Flists
+
+```bash
+# Enable flist uploads
+UPLOAD_MANIFESTS=true ./scripts/build.sh
+```
+
+Uploaded as:
+- `s3://{bucket}/{prefix}/manifests/modules-{VERSION}.fl`
+- `s3://{bucket}/{prefix}/manifests/firmware-{TAG}.fl`
+
+#### Requirements
+
+- MinIO Client (`mcli` or `mc`) must be installed
+- Valid S3 credentials in `config/rfs.conf`
+
 ### Container Builds
 
 Build in isolated container:
@@ -432,13 +503,16 @@ export DEBUG=1
 
 ```bash
 # Setup development environment
-./scripts/setup-dev.sh
+./scripts/dev-container.sh start
 
-# Run tests
+# Run incremental build
-./scripts/test.sh --all
+./scripts/build.sh
 
-# Check size impact
+# Test with QEMU
-./scripts/analyze-size.sh --compare
+./runit.sh --hypervisor qemu
+
+# Test with cloud-hypervisor
+./runit.sh --hypervisor ch
 ```
 
 ## License

claude.md

@@ -0,0 +1,523 @@
+# Claude Code Reference for Zero-OS Builder
+
+This document provides essential context for Claude Code (or any AI assistant) working with this Zero-OS Alpine Initramfs Builder repository.
+
+## Project Overview
+
+**What is this?**
+A sophisticated build system for creating custom Alpine Linux 3.22 x86_64 initramfs images with zinit process management, designed for Zero-OS deployment on ThreeFold Grid.
+
+**Key Features:**
+- Container-based reproducible builds (rootless podman/docker)
+- Incremental staged build pipeline with completion markers
+- zinit process manager (complete OpenRC replacement)
+- RFS (Remote File System) for lazy-loading modules/firmware from S3
+- Rust components built with musl static linking
+- Aggressive size optimization (strip + UPX)
+- Embedded initramfs in kernel (single vmlinuz.efi output)
+
+## Repository Structure
+
+```
+zosbuilder/
+├── config/                  # All configuration files
+│   ├── build.conf          # Build settings (versions, paths, flags)
+│   ├── packages.list       # Alpine packages to install
+│   ├── sources.conf        # ThreeFold components to build
+│   ├── modules.conf        # 2-stage kernel module loading
+│   ├── firmware.conf       # Firmware to include in initramfs
+│   ├── kernel.config       # Linux kernel configuration
+│   ├── init                # /init script for initramfs
+│   └── zinit/              # zinit service definitions (YAML)
+│
+├── scripts/
+│   ├── build.sh            # Main orchestrator (DO NOT EDIT LIGHTLY)
+│   ├── clean.sh            # Clean all artifacts
+│   ├── dev-container.sh    # Persistent dev container manager
+│   ├── rebuild-after-zinit.sh  # Quick rebuild helper
+│   ├── lib/                # Modular build libraries
+│   │   ├── common.sh       # Logging, path normalization, utilities
+│   │   ├── stages.sh       # Incremental stage tracking
+│   │   ├── docker.sh       # Container lifecycle
+│   │   ├── alpine.sh       # Alpine extraction, packages, cleanup
+│   │   ├── components.sh   # Build Rust components from sources.conf
+│   │   ├── initramfs.sh    # Assembly, optimization, CPIO creation
+│   │   └── kernel.sh       # Kernel download, config, build, embed
+│   └── rfs/                # RFS flist generation scripts
+│       ├── common.sh       # S3 config, version computation
+│       ├── pack-modules.sh # Create modules flist
+│       ├── pack-firmware.sh # Create firmware flist
+│       └── verify-flist.sh  # Inspect/test flists
+│
+├── docs/                   # Detailed documentation
+│   ├── NOTES.md           # Operational knowledge & troubleshooting
+│   ├── PROMPT.md          # Agent guidance (strict debugger mode)
+│   ├── TODO.md            # Persistent checklist with code refs
+│   ├── AGENTS.md          # Quick reference for agents
+│   ├── rfs-flists.md      # RFS design and runtime flow
+│   ├── review-rfs-integration.md  # Integration points
+│   └── depmod-behavior.md # Module dependency details
+│
+├── runit.sh               # Test runner (QEMU/cloud-hypervisor)
+├── initramfs/             # Generated initramfs tree
+├── components/            # Generated component sources
+├── kernel/                # Generated kernel source
+├── dist/                  # Final outputs
+│   ├── vmlinuz.efi        # Kernel with embedded initramfs
+│   └── initramfs.cpio.xz  # Standalone initramfs archive
+└── .build-stages/         # Incremental build markers (*.done files)
+```
+
+## Core Concepts
+
+### 1. Incremental Staged Builds
+
+**How it works:**
+- Each stage creates a `.build-stages/<stage_name>.done` marker on success
+- Subsequent builds skip completed stages unless forced
+- Use `./scripts/build.sh --show-stages` to see status
+- Use `./scripts/build.sh --rebuild-from=<stage>` to restart from a specific stage
+- Manually remove `.done` files to re-run specific stages
+
+**Build stages (in order):**
+```
+alpine_extract → alpine_configure → alpine_packages → alpine_firmware
+  → components_build → components_verify → kernel_modules
+  → init_script → components_copy → zinit_setup
+  → modules_setup → modules_copy → cleanup → rfs_flists
+  → validation → initramfs_create → initramfs_test → kernel_build
+```
+
+**Key insight:** The build ALWAYS runs inside a container. Host invocations auto-spawn containers.
+
+### 2. Container-First Architecture
+
+**Why containers?**
+- Reproducible toolchain (Alpine 3.22 base with exact dependencies)
+- Rootless execution (no privileged access needed)
+- Isolation from host environment
+- GitHub Actions compatible
+
+**Container modes:**
+- **Transient:** `./scripts/build.sh` spawns, builds, exits
+- **Persistent:** `./scripts/dev-container.sh start/shell/build`
+
+**Important:** Directory paths are normalized to absolute PROJECT_ROOT to avoid CWD issues when stages change directories (especially kernel builds).
+
+### 3. Component Build System
+
+**sources.conf format:**
+```
+TYPE:NAME:URL:VERSION:BUILD_FUNCTION[:EXTRA]
+```
+
+**Example:**
+```bash
+git:zinit:https://github.com/threefoldtech/zinit:master:build_zinit
+git:rfs:https://github.com/threefoldtech/rfs:development:build_rfs
+git:mycelium:https://github.com/threefoldtech/mycelium:0.6.1:build_mycelium
+release:corex:https://github.com/threefoldtech/corex/releases/download/2.1.4/corex-2.1.4-amd64-linux-static:2.1.4:install_corex:rename=corex
+```
+
+**Build functions** are defined in `scripts/lib/components.sh` and handle:
+- Rust builds with `x86_64-unknown-linux-musl` target
+- Static linking via `RUSTFLAGS="-C target-feature=+crt-static"`
+- Special cases (e.g., mycelium builds in `myceliumd/` subdirectory)
+
+### 4. RFS Flists (Remote File System)
+
+**Purpose:** Lazy-load kernel modules and firmware from S3 at runtime
+
+**Flow:**
+1. Build stage creates flists: `modules-<KERNEL_VERSION>.fl` and `firmware-<TAG>.fl`
+2. Flists are SQLite databases containing:
+   - Content-addressed blob references
+   - S3 store URIs (patched for read-only access)
+   - Directory tree metadata
+3. Flists embedded in initramfs at `/etc/rfs/`
+4. Runtime: zinit units mount flists over `/lib/modules/` and `/lib/firmware/`
+5. Dual udev coldplug: early (before RFS) for networking, post-RFS for new hardware
+
+**Key files:**
+- `scripts/rfs/pack-modules.sh` - Creates modules flist from container `/lib/modules/`
+- `scripts/rfs/pack-firmware.sh` - Creates firmware flist from Alpine packages
+- `config/zinit/init/modules.sh` - Runtime mount script
+- `config/zinit/init/firmware.sh` - Runtime mount script
+
+### 5. zinit Service Management
+
+**No OpenRC:** This system uses zinit exclusively for process management.
+
+**Service graph:**
+```
+/init → zinit → [stage1-modules, udevd, depmod]
+                → udev-trigger (early coldplug)
+                → network
+                → rfs-modules + rfs-firmware (mount flists)
+                → udev-rfs (post-RFS coldplug)
+                → services
+```
+
+**Service definitions:** YAML files in `config/zinit/` with `after:`, `needs:`, `wants:` dependencies
+
+### 6. Kernel Versioning and S3 Upload
+
+**Versioned Kernel Output:**
+- Standard kernel: `dist/vmlinuz.efi` (for compatibility)
+- Versioned kernel: `dist/vmlinuz-{VERSION}-{ZINIT_HASH}.efi`
+- Example: `vmlinuz-6.12.44-Zero-OS-a1b2c3d.efi`
+
+**Version components:**
+- `{VERSION}`: Full kernel version from `KERNEL_VERSION` + `CONFIG_LOCALVERSION`
+- `{ZINIT_HASH}`: Short git commit hash from `components/zinit/.git`
+
+**S3 Upload (optional):**
+- Controlled by `UPLOAD_KERNEL=true` environment variable
+- Uses MinIO client (`mcli` or `mc`) to upload to S3-compatible storage
+- Uploads versioned kernel to: `s3://{bucket}/{prefix}/kernel/{versioned_filename}`
+
+**Kernel Index Generation:**
+After uploading, automatically generates and uploads index files:
+- `kernels.txt` - Plain text, one kernel per line, sorted reverse chronologically
+- `kernels.json` - JSON format with metadata (timestamp, count)
+
+**Why index files?**
+- S3 web interfaces often don't support directory listings
+- Enables dropdown menus in web UIs without S3 API access
+- Provides kernel discovery for deployment tools
+
+**JSON index structure:**
+```json
+{
+  "kernels": ["vmlinuz-6.12.44-Zero-OS-abc1234.efi", ...],
+  "updated": "2025-01-04T12:00:00Z",
+  "count": 2
+}
+```
+
+**Key functions:**
+- `get_git_commit_hash()` in `scripts/lib/common.sh` - Extracts git hash
+- `kernel_build_with_initramfs()` in `scripts/lib/kernel.sh` - Creates versioned kernel
+- `kernel_upload_to_s3()` in `scripts/lib/kernel.sh` - Uploads to S3
+- `kernel_generate_index()` in `scripts/lib/kernel.sh` - Generates and uploads index
+
+## Critical Conventions
+
+### Path Normalization
+**Problem:** Stages can change CWD (kernel build uses `/workspace/kernel/current`)
+**Solution:** All paths normalized to absolute at startup in `scripts/lib/common.sh:244`
+
+**Variables affected:**
+- `INSTALL_DIR` (initramfs/)
+- `COMPONENTS_DIR` (components/)
+- `KERNEL_DIR` (kernel/)
+- `DIST_DIR` (dist/)
+
+**Never use relative paths** when calling functions that might be in different CWDs.
+
+### Branding and Security
+**Passwordless root enforcement:**
+- Applied in `scripts/lib/initramfs.sh:575` via `passwd -d -R "${initramfs_dir}" root`
+- Creates `root::` in `/etc/shadow` (empty password field)
+- Controlled by `ZEROOS_BRANDING` and `ZEROOS_PASSWORDLESS_ROOT` flags
+
+**Never edit /etc/shadow manually** - always use `passwd` or `chpasswd` with chroot.
+
+### Module Loading Strategy
+**2-stage approach:**
+- **Stage 1:** Critical boot modules (virtio, e1000, scsi) - loaded by zinit early
+- **Stage 2:** Extended hardware (igb, ixgbe, i40e) - loaded after network
+
+**Config:** `config/modules.conf` with `stage1:` and `stage2:` prefixes
+
+**Dependency resolution:**
+- Uses `modinfo` to build dependency tree
+- Resolves from container `/lib/modules/<FULL_VERSION>/`
+- Must run after `kernel_modules` stage
+
+### Firmware Policy
+**For initramfs:** `config/firmware.conf` is the SINGLE source of truth
+- Any firmware hints in `modules.conf` are IGNORED
+- Prevents duplication/version mismatches
+
+**For RFS:** Full Alpine `linux-firmware*` packages installed in container
+- Packed from container `/lib/firmware/`
+- Overmounts at runtime for extended hardware
+
+## Common Workflows
+
+### Full Build from Scratch
+```bash
+# Clean everything and rebuild
+./scripts/build.sh --clean
+
+# Or just rebuild all stages
+./scripts/build.sh --force-rebuild
+```
+
+### Quick Iteration After Config Changes
+```bash
+# After editing zinit configs, init script, or modules.conf
+./scripts/rebuild-after-zinit.sh
+
+# With kernel rebuild
+./scripts/rebuild-after-zinit.sh --with-kernel
+
+# Dry-run to see what changed
+./scripts/rebuild-after-zinit.sh --verify-only
+```
+
+### Minimal Manual Rebuild
+```bash
+# Remove specific stages
+rm -f .build-stages/initramfs_create.done
+rm -f .build-stages/validation.done
+
+# Rebuild only those stages
+DEBUG=1 ./scripts/build.sh
+```
+
+### Testing the Built Kernel
+```bash
+# QEMU (default)
+./runit.sh
+
+# cloud-hypervisor with 5 disks
+./runit.sh --hypervisor ch --disks 5 --reset
+
+# Custom memory and bridge
+./runit.sh --memory 4096 --bridge zosbr
+```
+
+### Persistent Dev Container
+```bash
+# Start persistent container
+./scripts/dev-container.sh start
+
+# Enter shell
+./scripts/dev-container.sh shell
+
+# Run build inside
+./scripts/dev-container.sh build
+
+# Stop container
+./scripts/dev-container.sh stop
+```
+
+## Debugging Guidelines
+
+### Diagnostics-First Approach
+**ALWAYS add diagnostics before fixes:**
+1. Enable `DEBUG=1` for verbose safe_execute logs
+2. Add strategic `log_debug` statements
+3. Confirm hypothesis in logs
+4. Then apply minimal fix
+
+**Example:**
+```bash
+# Bad: Guess and fix
+Edit file to fix suspected issue
+
+# Good: Diagnose first
+1. Add log_debug "Variable X=${X}, resolved=${resolved_path}"
+2. DEBUG=1 ./scripts/build.sh
+3. Confirm in output
+4. Apply fix with evidence
+```
+
+### Key Diagnostic Functions
+- `scripts/lib/common.sh`: `log_info`, `log_warn`, `log_error`, `log_debug`
+- `scripts/lib/initramfs.sh:820`: Validation debug prints (input, PWD, PROJECT_ROOT, resolved paths)
+- `scripts/lib/initramfs.sh:691`: Pre-CPIO sanity checks with file listings
+
+### Common Issues and Solutions
+
+**"Initramfs directory not found"**
+- **Cause:** INSTALL_DIR interpreted as relative in different CWD
+- **Fix:** Already patched - paths normalized at startup
+- **Check:** Look for "Validation debug:" logs showing resolved paths
+
+**"INITRAMFS_ARCHIVE unbound"**
+- **Cause:** Incremental build skipped initramfs_create stage
+- **Fix:** Already patched - stages default INITRAMFS_ARCHIVE if unset
+- **Check:** `scripts/build.sh:401` logs "defaulting INITRAMFS_ARCHIVE"
+
+**"Module dependency resolution fails"**
+- **Cause:** Container `/lib/modules/<FULL_VERSION>` missing or stale
+- **Fix:** `./scripts/rebuild-after-zinit.sh --refresh-container-mods`
+- **Check:** Ensure `kernel_modules` stage completed successfully
+
+**"Passwordless root not working"**
+- **Cause:** Branding disabled or shadow file not updated
+- **Fix:** Check ZEROOS_BRANDING=true in logs, verify /etc/shadow has `root::`
+- **Verify:** Extract initramfs and `grep '^root:' etc/shadow`
+
+## Important Files Quick Reference
+
+### Must-Read Before Editing
+- `scripts/build.sh` - Orchestrator with precise stage order
+- `scripts/lib/common.sh` - Path normalization, logging, utilities
+- `scripts/lib/stages.sh` - Stage tracking logic
+- `config/build.conf` - Version pins, directory settings, flags
+
+### Safe to Edit
+- `config/zinit/*.yaml` - Service definitions
+- `config/zinit/init/*.sh` - Runtime initialization scripts
+- `config/modules.conf` - Module lists (stage1/stage2)
+- `config/firmware.conf` - Initramfs firmware selection
+- `config/packages.list` - Alpine packages
+
+### Generated (Never Edit)
+- `initramfs/` - Assembled initramfs tree
+- `components/` - Downloaded component sources
+- `kernel/` - Kernel source tree
+- `dist/` - Build outputs
+- `.build-stages/` - Completion markers
+
+## Testing Architecture
+
+**No built-in tests during build** - Tests run separately via `runit.sh`
+
+**Why?**
+- Build is for assembly, not validation
+- Tests require hypervisor (QEMU/cloud-hypervisor)
+- Separation allows faster iteration
+
+**runit.sh features:**
+- Multi-disk support (qcow2 for QEMU, raw for cloud-hypervisor)
+- Network bridge/TAP configuration
+- Persistent volumes (reset with `--reset`)
+- Serial console logging
+
+## Quick Command Reference
+
+```bash
+# Build
+./scripts/build.sh                      # Incremental build
+./scripts/build.sh --clean             # Clean build
+./scripts/build.sh --show-stages       # Show completion status
+./scripts/build.sh --rebuild-from=zinit_setup  # Rebuild from stage
+DEBUG=1 ./scripts/build.sh             # Verbose output
+
+# Rebuild helpers
+./scripts/rebuild-after-zinit.sh       # After zinit/init/modules changes
+./scripts/rebuild-after-zinit.sh --with-kernel  # Also rebuild kernel
+./scripts/rebuild-after-zinit.sh --verify-only  # Dry-run
+
+# Testing
+./runit.sh                             # QEMU test
+./runit.sh --hypervisor ch             # cloud-hypervisor test
+./runit.sh --help                      # All options
+
+# Dev container
+./scripts/dev-container.sh start       # Start persistent container
+./scripts/dev-container.sh shell       # Enter shell
+./scripts/dev-container.sh build       # Build inside container
+./scripts/dev-container.sh stop        # Stop container
+
+# Cleanup
+./scripts/clean.sh                     # Remove all generated files
+rm -rf .build-stages/                  # Reset stage markers
+```
+
+## Environment Variables
+
+**Build control:**
+- `DEBUG=1` - Enable verbose logging
+- `FORCE_REBUILD=true` - Force rebuild all stages
+- `REBUILD_FROM_STAGE=<name>` - Rebuild from specific stage
+
+**Version overrides:**
+- `ALPINE_VERSION=3.22` - Alpine Linux version
+- `KERNEL_VERSION=6.12.44` - Linux kernel version
+- `RUST_TARGET=x86_64-unknown-linux-musl` - Rust compilation target
+
+**Firmware tagging:**
+- `FIRMWARE_TAG=20250908` - Firmware flist version tag
+
+**S3 upload control:**
+- `UPLOAD_KERNEL=true` - Upload versioned kernel to S3 (default: false)
+- `UPLOAD_MANIFESTS=true` - Upload RFS flists to S3 (default: false)
+- `KERNEL_SUBPATH=kernel` - S3 subpath for kernel uploads (default: kernel)
+
+**S3 configuration:**
+- See `config/rfs.conf` for S3 endpoint, credentials, paths
+- Used by both RFS flist uploads and kernel uploads
+
+## Documentation Hierarchy
+
+**Start here:**
+1. `README.md` - User-facing guide with features and setup
+2. This file (`claude.md`) - AI assistant context
+
+**For development:**
+3. `docs/NOTES.md` - Operational knowledge, troubleshooting
+4. `docs/AGENTS.md` - Quick agent reference
+5. `docs/TODO.md` - Current work checklist with code links
+
+**For deep dives:**
+6. `docs/PROMPT.md` - Strict debugger agent mode (diagnostics-first)
+7. `docs/rfs-flists.md` - RFS design and implementation
+8. `docs/review-rfs-integration.md` - Integration points analysis
+9. `docs/depmod-behavior.md` - Module dependency deep dive
+
+**Historical:**
+10. `IMPLEMENTATION_PLAN.md` - Original design document
+11. `GITHUB_ACTIONS.md` - CI/CD setup guide
+
+## Project Philosophy
+
+1. **Reproducibility:** Container-based builds ensure identical results
+2. **Incrementality:** Stage markers minimize rebuild time
+3. **Diagnostics-first:** Log before fixing, validate assumptions
+4. **Minimal intervention:** Alpine + zinit only, no systemd/OpenRC
+5. **Size-optimized:** Aggressive cleanup, strip, UPX compression
+6. **Remote-ready:** RFS enables lazy-loading for extended hardware support
+
+## Commit Message Guidelines
+
+**DO NOT add Claude Code or AI assistant references to commit messages.**
+
+Keep commits clean and professional:
+- Focus on what changed and why
+- Use conventional commit prefixes: `build:`, `docs:`, `fix:`, `feat:`, `refactor:`
+- Be concise but descriptive
+- No emoji unless project convention
+- No "Generated with Claude Code" or "Co-Authored-By: Claude" footers
+
+**Good example:**
+```
+build: remove testing.sh in favor of runit.sh
+
+Replace inline boot testing with standalone runit.sh runner.
+Tests now run separately from build pipeline for faster iteration.
+```
+
+**Bad example:**
+```
+build: remove testing.sh 🤖
+
+Made some changes to testing.
+
+🤖 Generated with [Claude Code](https://claude.com/claude-code)
+Co-Authored-By: Claude <noreply@anthropic.com>
+```
+
+## Keywords for Quick Search
+
+- **Build fails:** Check `DEBUG=1` logs, stage completion markers, container state
+- **Module issues:** `kernel_modules` stage, `CONTAINER_MODULES_PATH`, depmod logs
+- **Firmware missing:** `config/firmware.conf` for initramfs, RFS flist for runtime
+- **zinit problems:** Service YAML syntax, dependency order, init script errors
+- **Path errors:** Absolute path normalization in `common.sh:244`
+- **Size too large:** Check cleanup stage, strip/UPX execution, package list
+- **Container issues:** Rootless setup, subuid/subgid, podman vs docker
+- **RFS mount fails:** S3 credentials, network readiness, flist manifest paths
+- **Kernel upload:** `UPLOAD_KERNEL=true`, requires `config/rfs.conf`, MinIO client (`mcli`/`mc`)
+- **Kernel index:** Auto-generated `kernels.txt`/`kernels.json` for dropdown UIs, updated on upload
+
+---
+
+**Last updated:** 2025-01-04
+
+**Maintainer notes:** This file is the entry point for AI assistants. Keep it updated when architecture changes. Cross-reference with `docs/NOTES.md` for operational details.

config/build.conf

@@ -61,6 +61,7 @@ ENABLE_STRIP="true"
 ENABLE_UPX="true"
 ENABLE_AGGRESSIVE_CLEANUP="true"
 ENABLE_2STAGE_MODULES="true"
+UPLOAD_KERNEL=true
 
 # Debug and development
 DEBUG_DEFAULT="0"

config/sources.conf

@@ -4,7 +4,8 @@
 # Git repositories to clone and build
 git zinit https://github.com/threefoldtech/zinit master build_zinit
 git mycelium https://github.com/threefoldtech/mycelium v0.6.1 build_mycelium
-git zosstorage git@git.ourworld.tf:delandtj/zosstorage main build_zosstorage
+git zosstorage https://git.ourworld.tf/delandtj/zosstorage main build_zosstorage
+git youki git@github.com:youki-dev/youki.git v0.5.7 build_youki
 git rfs https://github.com/threefoldtech/rfs development build_rfs
 # Pre-built releases to download
 # release rfs https://github.com/threefoldtech/rfs/releases/download/v2.0.6/rfs v2.0.6 install_rfs

docs/NOTES.md

@@ -176,9 +176,12 @@ Stage System and Incremental Rebuilds
   - Shows stage status before/after marker removal; no --rebuild-from is passed by default (relies on markers only).
 - Manual minimal rebuild:
   - Remove relevant .done files, e.g.: initramfs_create.done initramfs_test.done validation.done
-  - Rerun: DEBUG=1 ./scripts/build.sh --skip-tests
+  - Rerun: DEBUG=1 ./scripts/build.sh
 - Show status:
   - ./scripts/build.sh --show-stages
+- Test built kernel:
+  - ./runit.sh --hypervisor qemu
+  - ./runit.sh --hypervisor ch --disks 5 --reset
 
 Key Decisions (current)
 - Firmware selection for initramfs comes exclusively from [config/firmware.conf](config/firmware.conf); firmware hints in modules.conf are ignored to avoid duplication/mismatch.

docs/PROMPT.md

@@ -107,7 +107,7 @@ Diagnostics-first workflow (strict)
 - For any failure, first collect specific logs:
   - Enable DEBUG=1 for verbose logs.
   - Re-run only the impacted stage if possible:
-    - Example: rm -f .build-stages/validation.done && DEBUG=1 ./scripts/build.sh --skip-tests
+    - Example: rm -f .build-stages/validation.done && DEBUG=1 ./scripts/build.sh
 - Use existing diagnostics:
   - Branding debug lines: [bash.initramfs_finalize_customization()](scripts/lib/initramfs.sh:575)
   - Validation debug lines (input, PWD, PROJECT_ROOT, INSTALL_DIR, resolved): [bash.initramfs_validate()](scripts/lib/initramfs.sh:799)
@@ -119,12 +119,15 @@ Common tasks and commands
   - DEBUG=1 ./scripts/build.sh
 - Minimal rebuild of last steps:
   - rm -f .build-stages/initramfs_create.done .build-stages/initramfs_test.done .build-stages/validation.done
-  - DEBUG=1 ./scripts/build.sh --skip-tests
+  - DEBUG=1 ./scripts/build.sh
 - Validation only:
   - rm -f .build-stages/validation.done
-  - DEBUG=1 ./scripts/build.sh --skip-tests
+  - DEBUG=1 ./scripts/build.sh
 - Show stage status:
   - ./scripts/build.sh --show-stages
+- Test built kernel:
+  - ./runit.sh --hypervisor qemu
+  - ./runit.sh --hypervisor ch --disks 5
 
 Checklists and helpers
 
@@ -154,7 +157,7 @@ C) Minimal rebuild after zinit/init/modules.conf changes
   - Stage status is printed before/after marker removal; the helper avoids --rebuild-from by default to prevent running early stages.
 - Manual fallback:
   - rm -f .build-stages/initramfs_create.done .build-stages/initramfs_test.done .build-stages/validation.done
-  - DEBUG=1 ./scripts/build.sh --skip-tests
+  - DEBUG=1 ./scripts/build.sh
 
 D) INITRAMFS_ARCHIVE unbound during kernel build stage
 - stage_kernel_build now defaults INITRAMFS_ARCHIVE if unset:

docs/TODO.md

@@ -57,7 +57,7 @@ This canonical checklist is the single source of truth for ongoing work. It mirr
   - Create: [bash.initramfs_create_cpio()](../scripts/lib/initramfs.sh:691)
   - Validate: [bash.initramfs_validate()](../scripts/lib/initramfs.sh:820)
 - [ ] QEMU / cloud-hypervisor smoke tests
-  - Test suite: [bash.testing_run_all()](../scripts/lib/testing.sh:299)
+  - Test runner: [runit.sh](../runit.sh)
 - [ ] Kernel embed path and versioning sanity
   - Embed config: [bash.kernel_modify_config_for_initramfs()](../scripts/lib/kernel.sh:130)
   - Full version logic: [bash.kernel_get_full_version()](../scripts/lib/kernel.sh:14)

docs/review-rfs-integration.md

@@ -13,7 +13,6 @@ Key sourced libraries:
 - [initramfs.sh](scripts/lib/initramfs.sh)
 - [stages.sh](scripts/lib/stages.sh)
 - [docker.sh](scripts/lib/docker.sh)
-- [testing.sh](scripts/lib/testing.sh)
 
 Main stages executed (incremental via [stage_run()](scripts/lib/stages.sh:99)):
 1) alpine_extract, alpine_configure, alpine_packages

scripts/build.sh

@@ -15,7 +15,6 @@ source "${SCRIPT_DIR}/lib/alpine.sh"
 source "${SCRIPT_DIR}/lib/components.sh"
 source "${SCRIPT_DIR}/lib/initramfs.sh"
 source "${SCRIPT_DIR}/lib/kernel.sh"
-source "${SCRIPT_DIR}/lib/testing.sh"
 
 # Build configuration loaded from config/build.conf via common.sh
 # Environment variables can override config file values
@@ -42,7 +41,6 @@ ZINIT_CONFIG_DIR="${CONFIG_DIR}/zinit"
 # Build options
 USE_CONTAINER="${USE_CONTAINER:-auto}"
 CLEAN_BUILD="${CLEAN_BUILD:-false}"
-SKIP_TESTS="${SKIP_TESTS:-false}"
 KEEP_ARTIFACTS="${KEEP_ARTIFACTS:-false}"
 
 # Display usage information
@@ -54,7 +52,6 @@ Usage: $0 [OPTIONS]
 
 Options:
   --clean              Clean build (remove all artifacts first)
-  --skip-tests         Skip boot tests
   --keep-artifacts     Keep build artifacts after completion
   --force-rebuild      Force rebuild all stages (ignore completion markers)
   --rebuild-from=STAGE Force rebuild from specific stage onward
@@ -92,10 +89,6 @@ function parse_arguments() {
                 CLEAN_BUILD="true"
                 shift
                 ;;
-            --skip-tests)
-                SKIP_TESTS="true"
-                shift
-                ;;
             --keep-artifacts)
                 KEEP_ARTIFACTS="true"
                 shift
@@ -408,20 +401,18 @@ function main_build_process() {
             log_debug "stage_kernel_build: defaulting INITRAMFS_ARCHIVE=${INITRAMFS_ARCHIVE}"
         fi
 
+        # Ensure FULL_KERNEL_VERSION is set for versioned output filename
+        if [[ -z "${FULL_KERNEL_VERSION:-}" ]]; then
+            FULL_KERNEL_VERSION=$(kernel_get_full_version "$KERNEL_VERSION" "$KERNEL_CONFIG")
+            export FULL_KERNEL_VERSION
+            log_debug "stage_kernel_build: resolved FULL_KERNEL_VERSION=${FULL_KERNEL_VERSION}"
+        fi
+
         kernel_build_with_initramfs "$KERNEL_CONFIG" "$INITRAMFS_ARCHIVE" "$kernel_output"
         export KERNEL_OUTPUT="$kernel_output"
     }
 
-    function stage_boot_tests() {
+    # Boot tests removed - use runit.sh for testing instead
-        if [[ "$SKIP_TESTS" != "true" ]]; then
-            # Ensure KERNEL_OUTPUT is set (for incremental builds)
-            if [[ -z "${KERNEL_OUTPUT:-}" ]]; then
-                KERNEL_OUTPUT="${DIST_DIR}/vmlinuz.efi"
-                export KERNEL_OUTPUT
-            fi
-            testing_run_all "$KERNEL_OUTPUT"
-        fi
-    }
 
     # Run all stages with incremental tracking
     stage_run "alpine_extract" stage_alpine_extract
@@ -442,7 +433,6 @@ function main_build_process() {
     stage_run "initramfs_create" stage_initramfs_create
     stage_run "initramfs_test" stage_initramfs_test
     stage_run "kernel_build" stage_kernel_build
-    stage_run "boot_tests" stage_boot_tests
 
     # Calculate build time
     local end_time=$(date +%s)
@@ -504,9 +494,6 @@ function main() {
 
         # Pass through relevant arguments to container
         local container_args=""
-        if [[ "$SKIP_TESTS" == "true" ]]; then
-            container_args="$container_args --skip-tests"
-        fi
         if [[ "$KEEP_ARTIFACTS" == "true" ]]; then
             container_args="$container_args --keep-artifacts"
         fi

scripts/dev-container.sh

@@ -18,7 +18,7 @@ export DEBUG="${DEBUG:-1}"
 source "${SCRIPT_DIR}/lib/common.sh"
 
 function show_usage() {
-    cat << EOF
+    cat <<EOF
 Zero OS Development Container Manager
 
 Usage: $0 [COMMAND]
@@ -94,6 +94,7 @@ function dev_container_start() {
         --name "$CONTAINER_NAME"
         --privileged
         -v "${PROJECT_ROOT}:/workspace"
+        -v "$HOME/.ssh:root/.ssh"
         -w /workspace
         -e DEBUG=1
         -e ALPINE_VERSION=3.22
@@ -252,7 +253,7 @@ function main() {
     logs)
         dev_container_logs
         ;;
-        help|--help|-h)
+    help | --help | -h)
         show_usage
         ;;
     *)

scripts/lib/common.sh

@@ -195,6 +195,26 @@ function get_file_size() {
     fi
 }
 
+# Get short git commit hash from a git repository directory
+function get_git_commit_hash() {
+    local repo_dir="$1"
+    local short="${2:-true}"  # Default to short hash
+
+    if [[ ! -d "$repo_dir/.git" ]]; then
+        echo "unknown"
+        return 1
+    fi
+
+    local hash
+    if [[ "$short" == "true" ]]; then
+        hash=$(cd "$repo_dir" && git rev-parse --short HEAD 2>/dev/null || echo "unknown")
+    else
+        hash=$(cd "$repo_dir" && git rev-parse HEAD 2>/dev/null || echo "unknown")
+    fi
+
+    echo "$hash"
+}
+
 # Wait for file to exist with timeout
 function wait_for_file() {
     local file="$1"

scripts/lib/components.sh

@@ -44,7 +44,7 @@ function components_parse_sources_conf() {
 
 		local type name url version build_func extra
 		# shellcheck disable=SC2086
-        read -r type name url version build_func extra <<< "$line"
+		read -r type name url version build_func extra <<<"$line"
 
 		if [[ -z "${type:-}" || -z "${name:-}" || -z "${url:-}" || -z "${version:-}" || -z "${build_func:-}" ]]; then
 			log_warn "Skipping malformed entry: ${_raw}"
@@ -68,7 +68,7 @@ function components_parse_sources_conf() {
 		esac
 
 		components_build_component "$name" "$build_func" "$components_dir"
-    done < "$sources_file"
+	done <"$sources_file"
 
 	if [[ $component_count -eq 0 ]]; then
 		log_warn "No components found in sources configuration"
@@ -239,13 +239,13 @@ function components_process_extra_options() {
 		log_info "Extracting archive: ${filename}"
 		safe_execute cd "$target_dir"
 		case "$filename" in
-            *.tar.gz|*.tgz)
+		*.tar.gz | *.tgz)
 			safe_execute tar -xzf "$filename"
 			;;
-            *.tar.bz2|*.tbz2)
+		*.tar.bz2 | *.tbz2)
 			safe_execute tar -xjf "$filename"
 			;;
-            *.tar.xz|*.txz)
+		*.tar.xz | *.txz)
 			safe_execute tar -xJf "$filename"
 			;;
 		*.zip)
@@ -465,6 +465,49 @@ function build_zosstorage() {
 	log_info "Built zosstorage binary (${binary_size}) at: ${binary_path}"
 }
 
+# Build function for youki (standard Rust build)
+function build_youki() {
+	local name="$1"
+	local component_dir="$2"
+
+	section_header "Building youki with musl target"
+
+	components_setup_rust_env
+
+	log_info "Building youki from: ${component_dir}"
+
+	if [[ ! -d "$component_dir" ]]; then
+		log_error "Component directory not found: ${component_dir}"
+		return 1
+	fi
+
+	log_info "Executing: cd $component_dir"
+	cd "$component_dir" || {
+		log_error "Failed to change to directory: $component_dir"
+		return 1
+	}
+
+	local current_dir
+	current_dir=$(pwd)
+	log_info "Current directory: ${current_dir}"
+
+	if [[ ! -f "Cargo.toml" ]]; then
+		log_error "Cargo.toml not found in: ${current_dir}"
+		return 1
+	fi
+
+	safe_execute cargo build --release --target "$RUST_TARGET"
+
+	local binary_path="target/${RUST_TARGET}/release/youki"
+	if [[ ! -f "$binary_path" ]]; then
+		log_error "youki binary not found at: ${binary_path}"
+		return 1
+	fi
+
+	local binary_size
+	binary_size=$(get_file_size "$binary_path")
+	log_info "Built youki binary (${binary_size}) at: ${binary_path}"
+}
 # Build function for mycelium (special subdirectory build)
 function build_mycelium() {
 	local name="$1"

scripts/lib/kernel.sh

@@ -224,12 +224,33 @@ function kernel_build_with_initramfs() {
     safe_mkdir "$output_dir"
     safe_copy "$kernel_image" "$output_abs"
 
+    # Also copy with versioned filename including kernel version and zinit hash
+    local full_kernel_version="${FULL_KERNEL_VERSION:-unknown}"
+    local zinit_hash="unknown"
+    local zinit_dir="${COMPONENTS_DIR:-${PROJECT_ROOT}/components}/zinit"
+
+    if [[ -d "$zinit_dir/.git" ]]; then
+        zinit_hash=$(get_git_commit_hash "$zinit_dir")
+    else
+        log_warn "zinit git directory not found at ${zinit_dir}, using 'unknown' for hash"
+    fi
+
+    # Create versioned filename: vmlinuz-{VERSION}-{ZINIT_HASH}.efi
+    local versioned_name="vmlinuz-${full_kernel_version}-${zinit_hash}.efi"
+    local versioned_output="${output_dir}/${versioned_name}"
+    safe_copy "$kernel_image" "$versioned_output"
+
     # Verify final kernel
     local kernel_size
     kernel_size=$(get_file_size "$output_abs")
+    local versioned_size
+    versioned_size=$(get_file_size "$versioned_output")
     log_info "Kernel build complete:"
     log_info "  Output file: ${output_abs}"
+    log_info "  Versioned:   ${versioned_output}"
     log_info "  Kernel size: ${kernel_size}"
+    log_info "  Version:     ${full_kernel_version}"
+    log_info "  zinit hash:  ${zinit_hash}"
 
     # Verify initramfs is embedded
     if strings "$output_file" | grep -q "initramfs"; then
@@ -237,6 +258,184 @@ function kernel_build_with_initramfs() {
     else
         log_warn "Initramfs embedding verification inconclusive"
     fi
+
+    # Upload versioned kernel to S3 if enabled
+    kernel_upload_to_s3 "$versioned_output" "$full_kernel_version" "$zinit_hash"
+}
+
+# Upload versioned kernel to S3 using MinIO client (mcli/mc)
+function kernel_upload_to_s3() {
+    local kernel_file="$1"
+    local kernel_version="$2"
+    local zinit_hash="$3"
+
+    section_header "Uploading Kernel to S3"
+
+    # Check if upload is enabled
+    if [[ "${UPLOAD_KERNEL:-false}" != "true" ]]; then
+        log_info "UPLOAD_KERNEL not enabled; skipping kernel upload"
+        return 0
+    fi
+
+    # Verify kernel file exists
+    if [[ ! -f "$kernel_file" ]]; then
+        log_error "Kernel file not found: ${kernel_file}"
+        return 1
+    fi
+
+    # Load S3 configuration from rfs.conf
+    local rfs_conf="${PROJECT_ROOT}/config/rfs.conf"
+    local rfs_conf_example="${PROJECT_ROOT}/config/rfs.conf.example"
+
+    if [[ -f "$rfs_conf" ]]; then
+        # shellcheck source=/dev/null
+        source "$rfs_conf"
+        log_info "Loaded S3 config from: ${rfs_conf}"
+    elif [[ -f "$rfs_conf_example" ]]; then
+        # shellcheck source=/dev/null
+        source "$rfs_conf_example"
+        log_warn "Using example S3 config: ${rfs_conf_example}"
+    else
+        log_error "No S3 config found (config/rfs.conf or config/rfs.conf.example)"
+        return 1
+    fi
+
+    # Validate required S3 variables
+    for var in S3_ENDPOINT S3_BUCKET S3_PREFIX S3_ACCESS_KEY S3_SECRET_KEY; do
+        if [[ -z "${!var}" ]]; then
+            log_error "Missing required S3 variable: ${var}"
+            return 1
+        fi
+    done
+
+    # Detect MinIO client binary (mcli or mc)
+    local mcli_bin=""
+    if command -v mcli >/dev/null 2>&1; then
+        mcli_bin="mcli"
+    elif command -v mc >/dev/null 2>&1; then
+        mcli_bin="mc"
+    else
+        log_warn "MinIO Client not found (expected mcli or mc); skipping kernel upload"
+        return 0
+    fi
+
+    log_info "Using MinIO client: ${mcli_bin}"
+
+    # Setup S3 alias
+    log_info "Configuring S3 alias..."
+    safe_execute "${mcli_bin}" alias set rfs "${S3_ENDPOINT}" "${S3_ACCESS_KEY}" "${S3_SECRET_KEY}"
+
+    # Construct destination path: rfs/{bucket}/{prefix}/kernel/{versioned_filename}
+    local kernel_filename
+    kernel_filename=$(basename "$kernel_file")
+    local kernel_subpath="${KERNEL_SUBPATH:-kernel}"
+    local mcli_dst="rfs/${S3_BUCKET}/${S3_PREFIX%/}/${kernel_subpath%/}/${kernel_filename}"
+
+    # Upload kernel
+    log_info "Uploading: ${kernel_file} -> ${mcli_dst}"
+    safe_execute "${mcli_bin}" cp "${kernel_file}" "${mcli_dst}"
+
+    log_info "✓ Kernel uploaded successfully"
+    log_info "  Version: ${kernel_version}"
+    log_info "  zinit:   ${zinit_hash}"
+    log_info "  S3 path: ${mcli_dst}"
+
+    # Generate and upload kernel index
+    kernel_generate_index "${mcli_bin}" "${S3_BUCKET}" "${S3_PREFIX}" "${kernel_subpath}"
+}
+
+# Generate kernel index file from S3 listing and upload it
+function kernel_generate_index() {
+    local mcli_bin="$1"
+    local bucket="$2"
+    local prefix="$3"
+    local kernel_subpath="$4"
+
+    section_header "Generating Kernel Index"
+
+    # Construct S3 path for listing
+    local s3_path="rfs/${bucket}/${prefix%/}/${kernel_subpath%/}/"
+
+    log_info "Listing kernels from: ${s3_path}"
+
+    # List all files in the kernel directory
+    local ls_output
+    if ! ls_output=$("${mcli_bin}" ls "${s3_path}" 2>&1); then
+        log_warn "Failed to list S3 kernel directory, index not generated"
+        log_debug "mcli ls output: ${ls_output}"
+        return 0
+    fi
+
+    # Parse output and extract kernel filenames matching vmlinuz-*
+    local kernels=()
+    while IFS= read -r line; do
+        # mcli ls output format: [DATE TIME TZ] SIZE FILENAME
+        # Extract filename (last field)
+        local filename
+        filename=$(echo "$line" | awk '{print $NF}')
+
+        # Filter for vmlinuz files (both .efi and without extension)
+        if [[ "$filename" =~ ^vmlinuz-.* ]]; then
+            kernels+=("$filename")
+        fi
+    done <<< "$ls_output"
+
+    if [[ ${#kernels[@]} -eq 0 ]]; then
+        log_warn "No kernels found in S3 path: ${s3_path}"
+        return 0
+    fi
+
+    log_info "Found ${#kernels[@]} kernel(s)"
+
+    # Create index files in dist directory
+    local index_dir="${DIST_DIR:-${PROJECT_ROOT}/dist}"
+    local text_index="${index_dir}/kernels.txt"
+    local json_index="${index_dir}/kernels.json"
+
+    # Generate text index (one kernel per line, sorted)
+    printf "%s\n" "${kernels[@]}" | sort -r > "$text_index"
+    log_info "Created text index: ${text_index}"
+
+    # Generate JSON index (array of kernel filenames)
+    {
+        echo "{"
+        echo "  \"kernels\": ["
+        local first=true
+        for kernel in $(printf "%s\n" "${kernels[@]}" | sort -r); do
+            if [[ "$first" == "true" ]]; then
+                first=false
+            else
+                echo ","
+            fi
+            printf "    \"%s\"" "$kernel"
+        done
+        echo ""
+        echo "  ],"
+        echo "  \"updated\": \"$(date -u +%Y-%m-%dT%H:%M:%SZ)\","
+        echo "  \"count\": ${#kernels[@]}"
+        echo "}"
+    } > "$json_index"
+    log_info "Created JSON index: ${json_index}"
+
+    # Upload both index files to S3
+    log_info "Uploading kernel index files to S3..."
+
+    local text_dst="${s3_path}kernels.txt"
+    local json_dst="${s3_path}kernels.json"
+
+    if safe_execute "${mcli_bin}" cp "$text_index" "$text_dst"; then
+        log_info "✓ Uploaded text index: ${text_dst}"
+    else
+        log_warn "Failed to upload text index"
+    fi
+
+    if safe_execute "${mcli_bin}" cp "$json_index" "$json_dst"; then
+        log_info "✓ Uploaded JSON index: ${json_dst}"
+    else
+        log_warn "Failed to upload JSON index"
+    fi
+
+    log_info "Kernel index generation complete"
 }
 
 # Build and install modules in container for proper dependency resolution

scripts/rebuild-after-zinit.sh

@@ -218,13 +218,9 @@ build_from_args=()
 
 if in_container; then
   # Run directly when already inside the dev/build container
-  if [[ "$run_tests" -eq 1 ]]; then
+  # Note: Tests are run separately using runit.sh, not during build
-    log "Including boot tests (in-container)"
+  log "Running rebuild (in-container) - use runit.sh for testing"
   DEBUG=1 "${PROJECT_ROOT}/scripts/build.sh" "${build_from_args[@]}" "${extra_args[@]}"
-  else
-    log "Skipping boot tests (in-container)"
-    DEBUG=1 "${PROJECT_ROOT}/scripts/build.sh" --skip-tests "${build_from_args[@]}" "${extra_args[@]}"
-  fi
 else
   # Not in container: delegate to dev-container manager which ensures container exists and is running
   devctl="${PROJECT_ROOT}/scripts/dev-container.sh"
@@ -234,11 +230,7 @@ else
     exit 1
   fi
 
-  if [[ "$run_tests" -eq 1 ]]; then
+  # Note: Tests are run separately using runit.sh, not during build
-    log "Including boot tests via dev-container"
+  log "Running rebuild via dev-container - use runit.sh for testing"
   "$devctl" build "${build_from_args[@]}" "${extra_args[@]}"
-  else
-    log "Skipping boot tests via dev-container"
-    "$devctl" build --skip-tests "${build_from_args[@]}" "${extra_args[@]}"
-  fi
 fi