docs: add CHANGELOG.md with project history

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: jayhesselberth

CHANGELOG.md

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+# Changelog
+
+All notable changes to the aa-tRNA-seq pipeline are documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
+
+## [Unreleased]
+
+### Added
+- Optional WarpDemuX barcode demultiplexing support for pooled/multiplexed sequencing runs (#74)
+- Optimized modkit thresholds from ModkitOpt
+- Pixi package manager support as primary environment manager
+- Mermaid diagram for workflow visualization
+
+### Changed
+- Updated README to use pixi instead of conda (#72)
+- Normalized file permissions across repository
+
+## [0.6.0] - 2025-11-07
+
+### Added
+- Claude Code session start hook for automated development setup (#69)
+- Comprehensive CI/CD build and test checks (#68)
+- New project initialization structure (#65)
+
+### Changed
+- Prefer pandas over polars for stability on some cluster nodes
+- Reduced Remora logging level
+
+## [0.5.0] - 2025-06-22
+
+### Added
+- LSF-specific cluster configuration (#63)
+
+### Changed
+- Renamed test directory to recommended `.tests/` location
+- Reduced and made optional dorado verbosity
+- Downgraded numpy to fix remora stats compatibility
+
+## [0.4.0] - 2025-03-16
+
+### Added
+- Modkit integration for RNA modification analysis (#59)
+  - `modkit_pileup` rule for modification pileups
+  - `modkit_summary` rule for modification summaries
+  - `modkit_extract` and `modkit_extract_full` rules for detailed modification data
+- Automatic dorado and model download/installation (#56)
+- Modified base calling support (pseU, m5C, inosine_m6A)
+- Full modkit outputs with optimized memory allocation
+
+### Changed
+- Eliminated support for FAST5 files - pipeline now POD5-only (#43)
+- Reorganized output directory structure
+- Renamed charging tags during transfer (ML→CL, MM→CM)
+- Updated model download strategy
+- Increased memory allocation for modkit rules
+
+### Fixed
+- Restored `-v` option in dorado for proper verbosity control
+
+## [0.3.0] - 2025-01-08
+
+### Added
+- Rule for calculating CPM of charged/uncharged tRNAs (#28)
+- Remora CCA classifier for charging state classification (#18)
+- GPU pipeline support for `cca_classify` rule (#23)
+- Charging probability extraction and analysis (#46)
+
+### Changed
+- Implemented ML threshold (≥200 = charged, <200 = uncharged)
+- Compressed output files for storage efficiency
+- Various tweaks to file handling (#27)
+
+### Fixed
+- Actually use the threshold value in classification
+
+## [0.2.0] - 2024-08-13
+
+### Added
+- Alignment filtering capabilities with configurable parameters (#13)
+- Optional Remora signal metrics extraction
+- Kmer models included in pipeline
+- Logging and optional failed BAM outputs
+- New BAM tag indicating why reads are filtered
+- Support for processing reads from both pass and fail directories
+
+### Changed
+- Cleanup filtering approach for full-length tRNA reads
+- Updated test data
+- Ignore supplementary and secondary alignments
+- Snakemake v8 compatibility (#10)
+
+### Fixed
+- Insertion double-counting bug (#15)
+- Dropped redundant summary align stats (#14)
+- Added 'pod5' to list of possible pod5 directories
+
+## [0.1.0] - 2024-05-19
+
+### Added
+- Support for merging multiple sequencing runs per sample
+- Support for unmapped BAM as input (#5)
+- Pipeline commit and config recording for reproducibility (#9)
+- Bedgraph output generation
+- Alignment statistics calculations
+- Base calling error frequency calculations
+
+### Changed
+- Use v5.0.0 dorado models with modification calling
+- Expose dorado and bwa command-line options
+- Reworked alignment stats output (#8)
+- Set rebasecalled outputs as read-only
+
+### Fixed
+- Keep additional BAM flags (e.g., pi) during processing (#1)
+- Use -T → -C options to preserve all BAM tags from dorado
+
+## [0.0.1] - 2024-02-07
+
+### Added
+- Initial pipeline release
+- Core workflow: POD5 merge → rebasecall → align → filter
+- BWA MEM alignment to tRNA + adapter reference
+- Post-alignment filtering for full-length tRNAs
+- Basic summary statistics generation
+- Snakemake workflow with modular rule structure
+- Conda environment specification
+- Sample configuration via TSV files