docs: Add comprehensive documentation and update planning

- Add docs/README.md with project overview and current status
- Add docs/architecture.md with detailed architecture documentation
- Add docs/development.md with development guide for contributors
- Update .notes/todo.md to reflect architecture fix completion
- Update .notes/plan.md with completed phases and next priorities

Architecture fixes (daemon and dbus), bubblewrap integration are now complete.
Ready for OCI integration phase.

scripts/install-daemon.sh

@@ -0,0 +1,135 @@
+#!/bin/bash
+# apt-ostree Daemon Installation Script
+# This script installs all daemon components for apt-ostree
+
+set -e
+
+# Colors for output
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+NC='\033[0m' # No Color
+
+# Function to print colored output
+print_status() {
+    echo -e "${GREEN}[INFO]${NC} $1"
+}
+
+print_warning() {
+    echo -e "${YELLOW}[WARNING]${NC} $1"
+}
+
+print_error() {
+    echo -e "${RED}[ERROR]${NC} $1"
+}
+
+# Check if running as root
+if [[ $EUID -ne 0 ]]; then
+   print_error "This script must be run as root"
+   exit 1
+fi
+
+print_status "Installing apt-ostree daemon components..."
+
+# Create necessary directories
+print_status "Creating directories..."
+mkdir -p /usr/libexec
+mkdir -p /etc/apt-ostree
+mkdir -p /var/lib/apt-ostree
+mkdir -p /var/cache/apt-ostree
+mkdir -p /var/log/apt-ostree
+mkdir -p /etc/dbus-1/system.d
+mkdir -p /usr/share/dbus-1/system-services
+mkdir -p /usr/share/polkit-1/actions
+
+# Copy daemon binary
+print_status "Installing daemon binary..."
+if [[ -f "target/release/apt-ostreed" ]]; then
+    cp target/release/apt-ostreed /usr/libexec/
+    chmod +x /usr/libexec/apt-ostreed
+else
+    print_warning "Daemon binary not found, skipping..."
+fi
+
+# Copy configuration files
+print_status "Installing configuration files..."
+cp src/daemon/apt-ostreed.conf /etc/apt-ostree/
+chmod 644 /etc/apt-ostree/apt-ostreed.conf
+
+# Copy D-Bus configuration
+print_status "Installing D-Bus configuration..."
+cp src/daemon/org.aptostree.dev.conf /etc/dbus-1/system.d/
+cp src/daemon/org.aptostree.dev.service /usr/share/dbus-1/system-services/
+chmod 644 /etc/dbus-1/system.d/org.aptostree.dev.conf
+chmod 644 /usr/share/dbus-1/system-services/org.aptostree.dev.service
+
+# Copy Polkit policy
+print_status "Installing Polkit policy..."
+cp src/daemon/org.aptostree.dev.policy /usr/share/polkit-1/actions/
+chmod 644 /usr/share/polkit-1/actions/org.aptostree.dev.policy
+
+# Copy systemd services
+print_status "Installing systemd services..."
+cp src/daemon/apt-ostreed.service /etc/systemd/system/
+cp src/daemon/apt-ostree-bootstatus.service /etc/systemd/system/
+cp src/daemon/apt-ostree-countme.service /etc/systemd/system/
+cp src/daemon/apt-ostree-countme.timer /etc/systemd/system/
+cp src/daemon/apt-ostreed-automatic.service /etc/systemd/system/
+cp src/daemon/apt-ostreed-automatic.timer /etc/systemd/system/
+
+chmod 644 /etc/systemd/system/apt-ostreed.service
+chmod 644 /etc/systemd/system/apt-ostree-bootstatus.service
+chmod 644 /etc/systemd/system/apt-ostree-countme.service
+chmod 644 /etc/systemd/system/apt-ostree-countme.timer
+chmod 644 /etc/systemd/system/apt-ostreed-automatic.service
+chmod 644 /etc/systemd/system/apt-ostreed-automatic.timer
+
+# Set proper ownership
+print_status "Setting ownership..."
+chown -R root:root /var/lib/apt-ostree
+chown -R root:root /var/cache/apt-ostree
+chown -R root:root /var/log/apt-ostree
+
+# Initialize OSTree repository if it doesn't exist
+if [[ ! -d "/var/lib/apt-ostree/repo/objects" ]]; then
+    print_status "Initializing OSTree repository..."
+    /usr/bin/ostree init --repo=/var/lib/apt-ostree/repo
+fi
+
+# Reload systemd and D-Bus
+print_status "Reloading systemd and D-Bus..."
+systemctl daemon-reload
+systemctl reload dbus
+
+# Enable services
+print_status "Enabling services..."
+systemctl enable apt-ostreed.service
+systemctl enable apt-ostree-bootstatus.service
+systemctl enable apt-ostree-countme.timer
+systemctl enable apt-ostreed-automatic.timer
+
+# Start the daemon
+print_status "Starting apt-ostreed daemon..."
+systemctl start apt-ostreed.service
+
+# Verify installation
+print_status "Verifying installation..."
+if systemctl is-active --quiet apt-ostreed.service; then
+    print_status "apt-ostreed daemon is running"
+else
+    print_error "apt-ostreed daemon failed to start"
+    systemctl status apt-ostreed.service
+    exit 1
+fi
+
+# Test D-Bus connection
+print_status "Testing D-Bus connection..."
+if gdbus introspect --system --dest org.aptostree.dev --object-path /org/aptostree/dev > /dev/null 2>&1; then
+    print_status "D-Bus connection successful"
+else
+    print_warning "D-Bus connection test failed"
+fi
+
+print_status "apt-ostree daemon installation completed successfully!"
+print_status "You can now use 'apt-ostree' commands with daemon support"
+print_status "Use 'systemctl status apt-ostreed.service' to check daemon status"