Major cleanup and optimization: Remove unused dependencies, clean build artifacts, and improve project structure

- Remove 7 unused dependencies: apt-pkg-native, pkg-config, walkdir, lazy_static, futures, async-trait, cap-std
- Delete dead code: Remove unused parallel.rs module
- Clean build artifacts: Remove debian/cargo/, debian/.debhelper/, and other build files
- Update .gitignore: Comprehensive patterns for build artifacts, test files, and temporary files
- Move documentation: Relocate project docs to docs/ directory
- Remove test artifacts: Clean up test files and package archives
- Update Cargo.toml: Streamline dependencies and remove unused features
- Verify build: Ensure project still compiles after cleanup

This commit significantly reduces project size and improves build efficiency.

.gitignore

@@ -4,11 +4,37 @@
 !/.notes/inspiration/readme.md
 */inspiration/
 inspiration
+
 # Rust build artifacts
 /target/
 **/*.rs.bk
 Cargo.lock
 
+# Debian build artifacts
+*.deb
+*.ddeb
+*.udeb
+debian/.debhelper/
+debian/cargo/
+debian/*.debhelper
+debian/debhelper-build-stamp
+debian/*.log
+debian/*.substvars
+debian/files
+debian/*.conffiles
+debian/*.postinst
+debian/*.postrm
+debian/*.prerm
+debian/*.triggers
+
+# Package archives and tarballs
+*.tar
+*.tar.gz
+*.tar.xz
+*.tar.bz2
+*.zip
+*.7z
+
 # IDE and editor files
 .vscode/
 .idea/
@@ -28,6 +54,7 @@ Thumbs.db
 # Logs
 *.log
 logs/
+debian/*.log
 
 # Temporary files
 *.tmp
@@ -43,3 +70,30 @@ tmp/
 # Trash
 .1trash/
 stubs.txt
+
+# Test artifacts
+test-*.log
+test-results/
+coverage/
+*.profraw
+*.profdata
+
+# Build stamps and cache
+*.stamp
+.cache/
+.cargo/registry/
+.cargo/git/
+
+# Generated documentation
+docs/_build/
+docs/.doctrees/
+docs/api/
+
+# Environment files
+.env
+.env.local
+.env.*.local
+
+# Local configuration
+config.local.*
+*.local

CHANGELOG.md

@@ -0,0 +1,103 @@
+# Changelog
+
+This file tracks changes made during development sessions. After each git commit, this file is cleared to start fresh.
+
+## Commands Enhanced
+- `shlib-backend` - Added real logic for shared library backend operations
+- `internals` - Enhanced with comprehensive system diagnostics and health checks
+- `apply-live` - Completed implementation for live system updates
+- `testutils` - Completed synthetic data generation and testing utilities
+
+## Features Added
+- Daemon functionality completed (DBus interface, transaction management, APT operations)
+- APT integration analysis completed (hardiness check)
+- APT tool blocking implementation guide created for debian-atomic project
+
+## Technical Improvements
+- Removed unused `apt-pkg-native` dependency from Cargo.toml
+- Verified all APT operations use command-line tools for reliability
+- Created comprehensive APT blocking implementation documentation
+- **Comprehensive .gitignore cleanup** - Added patterns for all build artifacts and test files
+- **Removed tracked build artifacts** - Cleaned up debian/cargo/, debian/.debhelper/, and package files
+
+## Files Modified
+- `src/daemon/dbus_new.rs` - Completed all DBus interface methods
+- `src/commands/shlib_backend.rs` - Added real implementation
+- `src/commands/internals.rs` - Enhanced with real system diagnostics
+- `src/commands/apply_live.rs` - Completed implementation
+- `src/commands/testutils.rs` - Completed implementation
+- `Cargo.toml` - Cleaned up unused dependencies
+- `apt-hardiness-report.md` - Created comprehensive APT integration report
+- `apt-tool-blocking-implementation.md` - Created implementation guide for debian-atomic
+- `.gitignore` - **COMPLETELY OVERHAULED** - Added comprehensive patterns for all build artifacts
+
+## Major Milestone Achieved
+- **Daemon Implementation Completed** ✅
+  - All DBus interface methods implemented
+  - Real transaction management working
+  - Real APT operations functional
+  - Client management system operational
+  - Update detection and configuration reload working
+
+## APT Integration Analysis Completed
+- **APT Hardiness Check** ✅
+  - Analyzed all APT-related commands and functionality
+  - Verified command-line approach is superior to library bindings
+  - Discovered `apt-pkg-native` was never actually used
+  - Confirmed hybrid command-line approach is optimal
+  - Created comprehensive report documenting findings
+
+## APT Tool Blocking Implementation Guide
+- **Created comprehensive guide** for debian-atomic project
+  - Explains how to block traditional APT tools on atomic systems
+  - Provides wrapper script implementations
+  - Details integration with deb-bootc-compose
+  - Includes testing and troubleshooting procedures
+  - Based on ublue-os DNF/YUM blocking approach
+
+## Unused Dependency Cleanup
+- **Removed `apt-pkg-native` dependency** from Cargo.toml
+- **Verified build still works** without the dependency
+- **Updated documentation** to reflect command-line APT integration approach
+- **Removed 6 additional unused dependencies**:
+  - `pkg-config` (both dependencies and build-dependencies)
+  - `walkdir` (file system operations)
+  - `lazy_static` (lazy initialization)
+  - `futures` (async utilities)
+  - `async-trait` (async trait support)
+  - `cap-std` and `cap-std-ext` (capability-based operations)
+- **Removed dead code** - deleted unused `parallel.rs` module
+- **Build verified working** after cleanup
+
+## Git Repository Cleanup
+- **Comprehensive .gitignore overhaul** ✅
+  - Added patterns for all Debian build artifacts (*.deb, debian/.debhelper/, debian/cargo/)
+  - Added patterns for package archives (*.tar, *.tar.gz, *.zip)
+  - Added patterns for test artifacts and build stamps
+  - Added patterns for environment and local configuration files
+- **Removed tracked build artifacts** ✅
+  - Cleaned up `debian/cargo/` (hundreds of build files)
+  - Cleaned up `debian/.debhelper/` (build helper files)
+  - Removed `quay.io_example_debian_latest.tar` (unclear purpose)
+  - Repository now properly ignores all build artifacts
+
+## Usage Instructions
+1. **Track changes** during development sessions
+2. **Copy relevant sections** to git commit messages
+3. **Run `./clear-changelog.sh`** after committing to reset for next session
+
+## Commit Message Format Example
+```
+feat: Complete daemon implementation and APT integration analysis
+
+- Implement all DBus interface methods for apt-ostreed
+- Complete transaction management and APT operations
+- Remove unused apt-pkg-native dependency
+- Create APT hardiness report confirming command-line approach
+- Add APT tool blocking implementation guide for debian-atomic
+
+Commands Enhanced: daemon (all methods), apply-live, testutils
+Features Added: Complete daemon functionality, APT analysis
+Technical Improvements: Dependency cleanup, APT integration validation
+Files Modified: dbus_new.rs, Cargo.toml, apt-hardiness-report.md, apt-tool-blocking-implementation.md
+```

Cargo.toml

@@ -9,15 +9,13 @@ keywords = ["apt", "ostree", "debian", "ubuntu", "package-management"]
 categories = ["system", "command-line-utilities"]
 
 [dependencies]
-# APT integration - using apt-pkg-native for better Debian Trixie compatibility
-apt-pkg-native = "0.3.3"
+# APT integration - using command-line tools (apt, apt-get, apt-cache, dpkg) for reliability and simplicity
 
 # OSTree integration
 ostree = "0.20.3"
 
 # System and FFI
 libc = "0.2"
-pkg-config = "0.3"
 num_cpus = "1.16"
 
 # Error handling
@@ -41,9 +39,6 @@ tracing-appender = "0.2"
 # Async runtime (used for concurrent operations)
 tokio = { version = "1.0", features = ["full"] }
 
-# File system operations
-walkdir = "2.4"
-
 # D-Bus integration (used for daemon communication)
 zbus = "4.0"
 zbus_macros = "4.0"
@@ -57,9 +52,6 @@ tar = "0.4"
 # Regular expressions
 regex = "1.0"
 
-# Lazy static initialization
-lazy_static = "1.4"
-
 # UUID generation
 uuid = { version = "1.0", features = ["v4"] }
 
@@ -73,18 +65,9 @@ polkit = "0.19"
 sha2 = "0.10"
 sha256 = "1.0"
 
-# Futures for async utilities
-futures = "0.3"
-async-trait = "0.1"
-
 # Development commands dependencies
 goblin = { version = "0.8", optional = true }           # ELF file manipulation
 rand = { version = "0.8", optional = true }             # Random number generation
-cap-std = { version = "1.0", optional = true }          # Capability-based file operations
-cap-std-ext = { version = "1.0", optional = true }      # Extended capability operations
-
-[build-dependencies]
-pkg-config = "0.3"
 
 [profile.release]
 opt-level = 3
@@ -97,8 +80,7 @@ debug = true
 
 [features]
 default = []
-development = ["goblin", "rand", "cap-std", "cap-std-ext"]
-dev-full = ["development", "cap-std", "cap-std-ext"]
+development = ["goblin", "rand"]
 
 [[bin]]
 name = "apt-ostree"

clear-changelog.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+
+# Clear the changelog file after git commit
+# Usage: ./clear-changelog.sh
+
+echo "Clearing changelog..."
+
+# Clear the changelog content but keep the structure
+cat > CHANGELOG.md << 'EOF'
+# Changelog
+
+This file tracks changes made during development sessions. After each git commit, this file is cleared to start fresh.
+
+## Current Session Changes
+
+### Commands Enhanced
+- 
+
+### Features Added
+- 
+
+### Technical Improvements
+- 
+
+### Files Modified
+- 
+
+## Usage
+
+1. **During Development**: Add brief notes about changes made
+2. **Before Commit**: Review changes and format for commit message
+3. **After Commit**: Clear this file to start fresh for next session
+
+## Commit Message Format
+
+Use the following format for commit messages:
+
+```
+feat: brief description of changes
+
+- Key change 1
+- Key change 2
+- Key change 3
+
+Files: file1.rs, file2.rs
+```
+EOF
+
+echo "Changelog cleared successfully!"
+echo "Ready for next development session."

debian/.debhelper/apt-ostree/dbgsym-build-ids

@@ -1 +0,0 @@
-11e903f528b383a5d007b7582e99c10bf23dc82c 66668761e4a15384e33d485af4dee8edd1705132 

debian/.debhelper/apt-ostree/dbgsym-root/DEBIAN/control

@@ -1,12 +0,0 @@
-Package: apt-ostree-dbgsym
-Source: apt-ostree
-Version: 0.1.0-2
-Auto-Built-Package: debug-symbols
-Architecture: amd64
-Maintainer: Robojerk <robojerk@example.com>
-Installed-Size: 2220
-Depends: apt-ostree (= 0.1.0-2)
-Section: debug
-Priority: optional
-Description: debug symbols for apt-ostree
-Build-Ids: 11e903f528b383a5d007b7582e99c10bf23dc82c 66668761e4a15384e33d485af4dee8edd1705132

debian/.debhelper/apt-ostree/dbgsym-root/DEBIAN/md5sums

@@ -1,2 +0,0 @@
-eaef3226264a9925619cf696c7f8864e  usr/lib/debug/.build-id/11/e903f528b383a5d007b7582e99c10bf23dc82c.debug
-b31fc1d6516de608be3ffa390c0826d0  usr/lib/debug/.build-id/66/668761e4a15384e33d485af4dee8edd1705132.debug

debian/.debhelper/apt-ostree/dbgsym-root/usr/share/doc/apt-ostree-dbgsym

@@ -1 +0,0 @@
-apt-ostree

debian/.debhelper/generated/apt-ostree/dh_installchangelogs.dch.trimmed

@@ -1,16 +0,0 @@
-apt-ostree (0.1.0-2) trixie; urgency=medium
-
-  * Updated for Debian Trixie/Forky compatibility
-  * Updated rust-apt dependency to 0.9.0 for libapt-pkg7.0 support
-  * Added explicit libapt-pkg7.0 dependency
-  * Fixed library compatibility issues
-
- -- Robojerk <robojerk@example.com>  Tue, 13 Aug 2025 18:40:00 +0000
-
-apt-ostree (0.1.0-1) trixie; urgency=medium
-
-  * Initial release
-  * Basic apt-ostree functionality
-  * Debian packaging support
-
- -- Robojerk <robojerk@example.com>  Tue, 13 Aug 2025 18:35:00 +0000 

debian/.debhelper/generated/apt-ostree/postinst.service

@@ -1,47 +0,0 @@
-# Automatically added by dh_installsystemd/13.24.2
-if [ "$1" = "configure" ] || [ "$1" = "abort-upgrade" ] || [ "$1" = "abort-deconfigure" ] || [ "$1" = "abort-remove" ] ; then
-	# The following line should be removed in trixie or trixie+1
-	deb-systemd-helper unmask 'apt-ostreed.service' >/dev/null || true
-
-	# was-enabled defaults to true, so new installations run enable.
-	if deb-systemd-helper --quiet was-enabled 'apt-ostreed.service'; then
-		# Enables the unit on first installation, creates new
-		# symlinks on upgrades if the unit file has changed.
-		deb-systemd-helper enable 'apt-ostreed.service' >/dev/null || true
-	else
-		# Update the statefile to add new symlinks (if any), which need to be
-		# cleaned up on purge. Also remove old symlinks.
-		deb-systemd-helper update-state 'apt-ostreed.service' >/dev/null || true
-	fi
-fi
-# End automatically added section
-# Automatically added by dh_installsystemd/13.24.2
-if [ "$1" = "configure" ] || [ "$1" = "abort-upgrade" ] || [ "$1" = "abort-deconfigure" ] || [ "$1" = "abort-remove" ] ; then
-	# The following line should be removed in trixie or trixie+1
-	deb-systemd-helper unmask 'apt-ostreed.socket' >/dev/null || true
-
-	# was-enabled defaults to true, so new installations run enable.
-	if deb-systemd-helper --quiet was-enabled 'apt-ostreed.socket'; then
-		# Enables the unit on first installation, creates new
-		# symlinks on upgrades if the unit file has changed.
-		deb-systemd-helper enable 'apt-ostreed.socket' >/dev/null || true
-	else
-		# Update the statefile to add new symlinks (if any), which need to be
-		# cleaned up on purge. Also remove old symlinks.
-		deb-systemd-helper update-state 'apt-ostreed.socket' >/dev/null || true
-	fi
-fi
-# End automatically added section
-# Automatically added by dh_installsystemd/13.24.2
-if [ "$1" = "configure" ] || [ "$1" = "abort-upgrade" ] || [ "$1" = "abort-deconfigure" ] || [ "$1" = "abort-remove" ] ; then
-	if [ -d /run/systemd/system ]; then
-		systemctl --system daemon-reload >/dev/null || true
-		if [ -n "$2" ]; then
-			_dh_action=restart
-		else
-			_dh_action=start
-		fi
-		deb-systemd-invoke $_dh_action 'apt-ostreed.service' 'apt-ostreed.socket' >/dev/null || true
-	fi
-fi
-# End automatically added section

debian/.debhelper/generated/apt-ostree/prerm.service

@@ -1,5 +0,0 @@
-# Automatically added by dh_installsystemd/13.24.2
-if [ -z "$DPKG_ROOT" ] && [ "$1" = remove ] && [ -d /run/systemd/system ] ; then
-	deb-systemd-invoke stop 'apt-ostreed.service' 'apt-ostreed.socket' >/dev/null || true
-fi
-# End automatically added section

debian/cargo/registry/CACHEDIR.TAG

@@ -1,3 +0,0 @@
-Signature: 8a477f597d28d172789f06886806bc55
-# This file is a cache directory tag created by cargo.
-# For information about cache directory tags see https://bford.info/cachedir/