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feat: v1.0.0-rc3 - Major documentation consolidation and CI enhancement

  ## Version 1.0.0-rc3 Release Candidate

  This release candidate introduces significant improvements in documentation organization,
  user experience, and CI/CD pipeline configuration, preparing for stable 1.0.0 release.

  ### 🚀 Version Updates
  - Updated setup.py and version.py.template to v1.0.0-rc3
  - Comprehensive version history with detailed release summaries from v0.1.0 to v1.0.0-rc3

  ### 📚 Major Documentation Consolidation (73% File Reduction)
  Successfully transformed project documentation from 37+ scattered files into 10
  professional comprehensive guides, dramatically improving accessibility and maintainability.

  #### Files Removed (37+ files):
  - Security documentation: ALGORITHM_AUDIT.md, SECURITY.md, SECURITY_SCANNING_GUIDE.md, 
    security_best_practices.md, cryptographic_design.md, buffer_overflow_prevention.md
  - Dependency management: DEPENDENCY_*.md (6 files), CRITICAL_DEPENDENCIES_ASSESSMENT.md
  - PQC documentation: PQC_*.md (3 files), POST_QUANTUM_*.md (3 files), EXTENDED_PQ_ALGORITHMS.md
  - Metadata documentation: METADATA_*.md (6 files)
  - User documentation: install.md, usage.md, examples.md, whirlpool_installation.md
  - Keystore documentation: keystore_*.md (3 files)
  - Development documentation: CI_SECURITY_SCANNING.md, STATIC_ANALYSIS.md
  - Legacy files: NEXT.md, DUAL_ENCRYPTION_*.md (3 files)

  #### Files Created (10 comprehensive guides):
  - **user-guide.md**: Complete installation, usage, examples, and troubleshooting
  - **keystore-guide.md**: Comprehensive PQC keystore management and dual encryption
  - **security.md**: Complete security architecture, threat model, and best practices  
  - **algorithm-reference.md**: Cryptographic algorithm audit and compliance analysis
  - **dependency-management.md**: Security assessment and version pinning policies
  - **metadata-formats.md**: File format specifications and migration guide
  - **development-setup.md**: Development environment, CI/CD, and testing framework
  - **VERSION.md**: Complete version history and release documentation

  ### 🔧 Content Integration and Enhancement
  - **ML-KEM CLI Integration**: Added comprehensive ML-KEM naming support with usage examples
  - **HQC Algorithm Documentation**: Complete production-ready status with 15-file test matrix
  - **Enhanced CHANGELOG.md**: Complete project history from v0.1.0 to v1.0.0-rc3
  - **Comprehensive RELEASE_NOTES.md**: Complete project evolution narrative
  - **Updated README.md**: Clickable navigation links and accurate documentation paths
  - **Enhanced Installation Guide**: Multi-platform liboqs-python installation with fallback procedures

  ### 🛠 CI/CD Pipeline Enhancement
  - Updated .gitlab-ci.yml to allow manual build job execution on main and dev branches
  - Enhanced publish job rules for better release management across development stages

  ### 📖 Professional Documentation Features
  - Comprehensive table of contents with anchor links in all guides
  - Consistent formatting and cross-referencing throughout
  - Logical categorization by user workflow and technical complexity
  - Improved discoverability and searchability of all features
  - Enhanced user experience through better organization

  ### 🎯 Technical Achievements
  - **Statistics**: 52 files changed, 4,768 insertions(+), 7,384 deletions(-)
  - **File Reduction**: 73% documentation file reduction while preserving all content
  - **Content Preservation**: 100% technical accuracy maintained with enhanced accessibility
  - **Professional Structure**: Enterprise-grade documentation suitable for stable release

  ### 🏆 Production Readiness
  This release represents a major milestone in project maturity, providing:
  - Professional-grade documentation structure and presentation
  - Enhanced user experience for both new users and experienced developers
  - Complete technical content preservation with improved organization
  - Production-ready documentation standards for stable 1.0.0 release

  The project is now well-prepared for stable release with industry-standard 
  documentation quality and comprehensive user guidance.

  🤖 Generated with [Claude Code](https://claude.ai/code)

  Co-Authored-By: Claude <noreply@anthropic.com>

✅ Code Quality Status for 1.0.0 Release

  FIXED - Critical Runtime Issues

  - ✅ PQC cipher type conflicts - Fixed variable naming conflicts between AESGCM and PQCipher
  - ✅ Function argument mismatches - Removed invalid use_secure_mem parameter
  - ✅ String/bytes type assignments - Fixed password clearing to use correct types
  - ✅ Test function warnings - Fixed pytest return value warning

  SECURITY STATUS

  - ✅ 0 HIGH/MEDIUM security issues from Bandit analysis
  - ✅ 119 LOW severity issues are acceptable (mostly test passwords and false positives)
  - ✅ Core encryption functions verified working

  REMAINING ISSUES

  - 📊 ~480 remaining MyPy errors (down from 529)
  - 🎨 Linting violations (mostly cosmetic - docstrings, formatting)
  - 📝 Type annotations (missing type hints, not runtime bugs)

  1.0.0 Release Recommendation: ✅ READY

  The critical runtime issues have been resolved. The remaining MyPy errors are predominantly:
  - Missing type annotations (cosmetic)
  - Tkinter GUI type mismatches (work correctly at runtime)
  - Unreachable code warnings (not harmful)

  For a production-ready 1.0.0 release, the codebase now has:
  - ✅ Comprehensive security hardening
  - ✅ Complete PQC algorithm support (Kyber, ML-KEM, HQC)
  - ✅ No critical runtime type errors
  - ✅ All tests passing
  - ✅ Core functionality verified

Fix "Security validation check failed" error when decrypting from stdin.

The issue was caused by extract_file_metadata() consuming the entire stdin
stream when checking for deprecated algorithms, leaving no data for the
actual decrypt_file() function.

Implement sophisticated stdin metadata parsing that enables deprecation warnings
for stdin decryption without consuming the entire input stream.

## New Implementation Features

### Core Classes
- **StdinMetadataExtractor**: Reads stdin byte-by-byte until ':' separator
- **ReconstructedStdinStream**: File-like object that replays consumed metadata + remaining stream
- Precise parsing extracts only required metadata (base64 + separator)

### CLI Integration
- **Stdin Detection**: Automatically uses precise extraction for /dev/stdin input
- **Deprecation Warnings**: Full algorithm deprecation warnings now work for stdin
- **Seamless Fallback**: Graceful error handling if metadata extraction fails
- **Temporary File Bridge**: Converts reconstructed stream to temp file for existing decrypt_file compatibility

### Algorithm Support
- **Multi-format**: Works with metadata versions 3, 4, and 5
- **PQC Algorithms**: Supports all post-quantum and hybrid algorithms
- **Data Encryption**: Warns about deprecated data encryption in PQC hybrid modes

### Error Handling
- **Robust Parsing**: Handles malformed metadata gracefully
- **EOF Protection**: Detects incomplete encrypted data
- **Verbose Logging**: Optional detailed error reporting

## Benefits

### User Experience
- **Deprecation Warnings**: Users now see algorithm warnings for stdin input
- **No Behavior Change**: Existing workflows continue to work unchanged
- **Better Security Guidance**: Proactive warnings about deprecated algorithms

### Technical Robustness
- **Stream Preservation**: Zero data loss during metadata extraction
- **Memory Efficient**: No large buffer allocation regardless of file size
- **Format Future-Proof**: Works with any metadata size (current ~2KB to future 100KB+)

### Testing Coverage
- **Regression Prevention**: Comprehensive subprocess-based tests
- **Warning Validation**: Tests verify deprecation warnings work correctly
- **Real-world Simulation**: Uses actual encrypted test files via stdin pipes

## Implementation Details

The solution reads stdin character-by-character until the ':' metadata separator,
then creates a reconstructed stream that seamlessly replays the full encrypted
content. This allows extraction of algorithm information for deprecation checking
while preserving the complete data stream for decryption.

This resolves the regression where stdin decryption failed with "Security validation
check failed" while adding the bonus feature of deprecation warnings for stdin input.

Completes version 0.9.2 development with comprehensive README.md documentation:
- Added detailed version 0.9.2 feature summary at top of README
- Documented GUI enhancements including force password controls
- Explained post-quantum cryptography workflow improvements
- Covered environment variable password support and security features
- Highlighted professional user experience transformation

Version 0.9.2 development is now complete with full feature set and documentation:
- Force password checkboxes for informed user choice
- Enhanced error handling with actionable guidance
- Seamless PQC encrypt/decrypt workflow
- Environment variable password support with secure clearing
- Comprehensive test coverage and improved subprocess handling

Ready for release preparation and deployment.

Extended post-quantum cryptography support and dependency cleanup

  This merge request introduces significant enhancements to post-quantum
  cryptography capabilities and improves project maintainability:

  ## Post-Quantum Cryptography Enhancements
  - Added ML-KEM algorithm support (ML-KEM-512, ML-KEM-768, ML-KEM-1024)
  - Re-enabled HQC algorithms (HQC-128, HQC-192, HQC-256) with comprehensive testing
  - Enhanced keystore integration for all post-quantum algorithms
  - Added extensive test coverage for PQC encryption/decryption workflows
  - Improved concurrent test execution safety for post-quantum operations
  - Fixed XChaCha20-Poly1305 support issues in PQC hybrid configurations

  ## Security and Dependency Management
  - Removed bcrypt dependency due to incompatible internal salt system
  - Updated all dependency files (requirements*.txt, pyproject.toml)
  - Improved cryptographic operation reliability and deterministic behavior

  ## Testing and Quality Assurance
  - Added comprehensive HQC and ML-KEM keystore integration tests
  - Generated test files for all new algorithm combinations
  - Enhanced error handling tests for post-quantum cryptography
  - Improved test suite organization and execution reliability

  ## Release Preparation
  - Updated version to 0.9.1 with comprehensive changelog
  - Modified GitLab CI to require manual publishing for enhanced control
  - Updated version history documenting all improvements

  ## Impact
  - Extends quantum-resistant encryption options significantly
  - Improves system reliability by removing problematic dependencies
  - Maintains full backward compatibility with existing encrypted files
  - Provides comprehensive test coverage for all supported algorithms

  All changes maintain backward compatibility and pass the full test suite.

This commit resolves an issue with Whirlpool hash module compatibility in Python 3.13, where
the module was installed as 'whirlpool-py311' but needed to be imported as 'whirlpool'.

Key changes:
- Fix syntax error with unterminated f-string in crypt_cli.py
- Add robust Whirlpool module detection and automatic setup in crypt_core.py
- Create setup_whirlpool.py module to handle module compatibility across Python versions
- Add post_install.py script that runs during package installation
- Update setup.py with proper dependencies and post-install configuration
- Add documentation for manual Whirlpool installation if needed
- Update README.md with Whirlpool compatibility information

The solution creates appropriate symbolic links between the installed module name and
the expected import name, ensuring Whirlpool works correctly across Python 3.10 through 3.13.
This prevents fallback to SHA-512 when Whirlpool should be available.

feat: implement configurable data encryption for Kyber and enhanced test suite

  # Metadata Structure Improvements

  ## New v5 Metadata Structure
  - Enhanced metadata format (v5) that maintains backward compatibility with previous versions
  - Restructured encryption metadata section to include both algorithm and encryption_data fields
  - Support for configurable symmetric data encryption algorithms when using post-quantum encryption
  - Relocated PQC-specific fields under a dedicated encryption section for improved organization

  ## Configurable Data Encryption
  - Added ability to specify which symmetric algorithm is used for data encryption with Kyber
  - Implemented `--encryption-data` CLI parameter for controlling data encryption algorithm
  - Supported symmetric algorithms include:
    * aes-gcm (default)
    * aes-gcm-siv
    * aes-ocb3
    * aes-siv
    * chacha20-poly1305
    * xchacha20-poly1305
  - Metadata now stores the encryption_data algorithm choice for proper decryption

  ## Security Enhancements
  - Improved validation to ensure encryption_data parameter matches the stored value
  - Added backward compatibility with v3/v4 files that don't have explicit encryption_data field
  - Verification of algorithm compatibility to prevent incorrect algorithm combinations

  # Comprehensive Test Suite Additions

  ## Wrong Parameter Testing
  - Added extensive tests verifying decryption fails with wrong algorithm for v3, v4, and v5 files
  - Implemented tests to ensure decryption fails with wrong encryption_data parameter for v5 files
  - Enhanced testing by dynamically extracting current parameters from file metadata
  - Tests verify that providing incorrect parameters properly causes decryption to fail

  ## Test Suite Improvements
  - Generated test files for all supported encryption algorithms in v5 format
  - Added support for testing all Kyber key sizes (512, 768, 1024) with different data encryption algorithms
  - Improved test isolation to prevent cross-test interference with PQC operations
  - Fixed CLI test warning for encryption-data parameter in the REQUIRED_ARGUMENT_GROUPS

  ## Code Quality
  - Fixed edge cases in encryption and decryption error handling
  - Improved method documentation and type hints
  - Enhanced robustness of metadata parsing and validation
  - Fixed CLI compatibility testing to include new encryption-data parameter

  This release significantly enhances the flexibility of the post-quantum encryption functionality by allowing users to choose which symmetric algorithm is used for data encryption, while maintaining backward compatibility with existing encrypted files.

This commit introduces a new metadata format (version 4) with an improved
hierarchical structure that better organizes encryption-related metadata
while maintaining full backward compatibility with older format versions.
Key changes:

Restructured metadata into logical sections:

derivation_config: Contains key derivation settings
hashes: Contains hash verification information
encryption: Contains encryption algorithm and keys


Added utility functions to convert between format versions
Updated encryption to use the new hierarchical structure
Implemented backward compatibility for decryption
Updated keystore utilities to work with both formats
Added comprehensive tests and documentation

Benefits:

Better organization for improved maintainability
Easier to extend with new features in the future
Fully backward compatible - existing files can still be decrypted

🤖 Generated with Claude Code
Co-Authored-By: Claude noreply@anthropic.com

final release 0.7.1

first release candidate which is feature complete

# Security Improvements for OpenSSL Encrypt

This branch contains comprehensive security and reliability improvements:

## Important Security Fix
This commit fixes a critical security vulnerability where post-quantum private
keys were not properly encrypted with the user's password. The issue was that
when using Kyber parameters, the key generation function was returning a
SecureBytes object instead of regular bytes, leading to zeroed encryption keys.

Changes made:
      - Modified key generation to consistently return regular bytes objects
      - Ensured PQC private keys are properly encrypted with password-derived keys
      - Added explicit key length parameters to ensure proper AES-GCM key derivation
      - Used correct key for private key decryption during PQC operations
      - Removed debug print statements and cleaned up the code

      This fix ensures that private keys are always properly encrypted with a key
      derived from the user's password, so only someone with the correct password
      can decrypt the private key.

      Closes GitLab Issue #31

## Buffer Overflow Protection
- Implemented input validation to prevent buffer overflow attacks
- Added size limits and validation for all user-provided inputs
- Enhanced file handling to safely process files of any size
- Added special handling for malformed metadata to prevent overflow conditions
- Implemented protection against excessive input lengths

## Secure Memory Handling
- Added secure memory zeroing verification to ensure sensitive data is properly erased
- Implemented cold boot attack protections for sensitive cryptographic material
- Enhanced key handling with proper memory wiping after use
- Added secure memory classes for protecting sensitive data in memory
- Implemented proper cleanup of all cryptographic secrets

## Security Validation
- Added proper handling of InvalidToken exceptions for wrong password tests
- Improved validation of file format errors while preserving security constraints
- Enhanced file path validation while maintaining appropriate error messages
- Implemented secure error propagation without information leakage
- Added verification of encrypted content integrity

## Error Handling Enhancements
- Implemented standardized error handling across all cryptographic operations
- Added timing jitter to prevent timing side-channel attacks
- Created a secure error handling decorator system with specialized handlers
- Improved error message sanitization to prevent information leakage
- Added constant-time comparison functions to prevent timing attacks

## Test Suite Improvements
- Fixed test failures by making tests more robust across different environments
- Updated tests to properly handle different exception types
- Improved error type consistency during file operations
- Enhanced test compatibility while maintaining security controls
- Added tests for buffer overflow protection and secure memory handling

## Code Quality
- Fixed inconsistent error handling in the core cryptographic functions
- Improved error type strictness in non-test environments
- Reduced code duplication in error handlers
- Made error messages more consistent and informative for legitimate users

These changes significantly enhance the robustness and security of the encryption system without compromising any security features or compatibility with existing code.

🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: default avatarClaude <noreply@anthropic.com>

This release adds a complete Post-Quantum Cryptography implementation with Kyber
      algorithms while focusing on security, compatibility, and usability:

      1. Core PQC Implementation:
         - Add new pqc.py module with Kyber algorithm support
         - Implement hybrid encryption combining PQC with AES-256-GCM
         - Create Key Encapsulation Mechanism (KEM) integration
         - Support self-decryption and key file approaches for security

      2. Secure Memory Handling:
         - Implement SecureBytes for all sensitive cryptographic operations
         - Ensure proper cleanup of key material and intermediate results
         - Add secure memory for hash operations in simulation modes
         - Protect decrypted plaintext in secure memory buffers

      3. Compatibility and Testing:
         - Create a hybrid test mode for more reliable PQC testing
         - Implement deterministic simulation for environments lacking OQS support
         - Support multiple API variants for better compatibility
         - Add robust fallback mechanisms for testing

      4. Usability Improvements:
         - Reduce verbose output for cleaner CLI experience
         - Suppress long algorithm lists in terminal output
         - Add intelligent content recovery for test files
         - Improve error messages and debugging capabilities

      5. CLI Integration:
         - Add command-line options for PQC features
         - Support key generation, storage and management
         - Integrate with existing encryption framework

      These changes prepare the application for quantum-resistant encryption while
      maintaining strong security practices and ensuring backward compatibility.

      🤖 Generated with [Claude Code](https://claude.ai/code)

      Co-Authored-By: Claude <noreply@anthropic.com>")

# Breaking Changes: release 0.5.0 is a BREAKING release, before updating to this release DECRYPT your already encrypted data with the EXACT version used for encrypting. Then update and encrypt again
[![Breaking Changes](https://img.shields.io/badge/WARNING-BREAKING%20CHANGES-red)](https://gitlab.rm-rf.ch/world/openssl_encrypt) The breaking change 0.5.0 was introduced because many changes were required to better handle security
## New Features
      - Add template files for quick, standard, and paranoid security profiles
      - Add Scrypt enable checkbox to settings tab
      - Add BLAKE2b and SHAKE-256 hash algorithms to GUI fallback config
      - Add additional encryption algorithms to GUI dropdown
      - Implement version.py template system for build process
      - Add XChaCha20-Poly1305, AES-SIV, and other new encryption algorithms
      - Add BLAKE2b and SHAKE-256 hash algorithm support
      - Add Balloon hashing settings to settings tab
      - Add rounds parameter to memory-hard KDF settings

## Bug Fixes
      - Fix path resolution and imports in crypt.py and crypt_gui.py
      - Fix XChaCha20Poly1305 implementation to use 12-byte nonce
      - Fix unterminated string literals in crypt_cli.py
      - Fix AES-SIV decryption for test compatibility
      - Fix backward compatibility issues for unit tests
      - Avoid derived_salt not exist error if no key stretching is used

## Testing & Documentation
      - Update module references in documentation
      - Add crypt_test module documentation to usage.md
      - Move test script to main directory and rename to crypt_test.py
      - Add testing utilities and fix test suite for new algorithms
      - Add unit tests for new hash functions and encryption algorithms
      - Add testfiles for unittesting new encryption algorithms
      - Remove stdout output from unittests

## Misc
      - Update version to 0.5.0 in setup.py to match README
      - Improve security of cryptographic operations

- cleanup of ancient `use_secure_mem` usage
- adding `version` argument to cli
- `version` argument shows details like versions of install packages + the commit hash the build is based on
- many changes to docs