⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

autodoc/docmd/pkg_obitools_obiconvert.md

@@ -0,0 +1,62 @@
+# `obiconvert`: Semantic Overview of Public Functionalities
+
+The `obiconvert` package provides a robust, CLI-driven framework for converting and managing biological sequence data within the OBITools4 ecosystem. It enables format-agnostic input parsing, standardized output generation (FASTA/FASTQ/JSON), and configurable preprocessing—while preserving metadata semantics.
+
+## Input Handling
+
+- **`ExpandListOfFiles(check_ext bool, filenames ...string) []string`**  
+  Expands file paths into a deduplicated list of eligible files. Supports local directories, symlinks (resolved), and remote URLs (`http(s)://`, `ftp://`).  
+  When `check_ext=true`, filters files by extension: `.fasta[.gz]`, `.fastq[.fq][.gz]`, `.seq[.gz]`, `.gb[| gbff | dat ][.gz]`, and `.ecopcr[.gz]`.
+
+- **`CLIReadBioSequences(filenames ...string) obiiter.IBioSequence`**  
+  Returns a lazy, streaming iterator over biological sequences from files or stdin. Automatically selects parsing strategy based on CLI flags:
+  - JSON-style (`--input-json-header`)
+  - OBI-compliant headers (`--input-OBI-header`, `--input-obi`)
+  - Heuristic auto-detection (default).
+  
+  Configurable via CLI options:
+  - Parallel workers (`nworkers ≥ 2`)
+  - Batch size and memory limits
+  - `U→T` conversion for RNA (`--u-to-t`)
+  - Skip empty sequences (`--skip-empty`)
+  
+  Handles:
+  - Single/multiple files (with batched parallel reading)
+  - Paired-end input via `--paired-with`
+  - Fallback readers: FASTA, FASTQ, GenBank/EMBL, ecoPCR output, CSV
+
+- **`OpenSequenceDataErrorMessage(args ...string, err error)`**  
+  Formats and logs user-friendly errors for input failures (stdin-only / single-file / multi-file), then exits with status `1`.
+
+## Output Handling
+
+- **`CLIWriteBioSequences(iter obiiter.IBioSequence, filenames ...string)`**  
+  Writes sequences from an `IBioSequence` iterator to stdout or files, based on CLI options:
+  - **Format**: FASTQ (if quality scores present), FASTA, JSON (default), or generic sequence.
+  - **Header style**: Configured via `CLIOutputFastHeaderFormat()` → `"json"` or `"obi"`.
+  - **Compression**: Optional gzip (`--gzip`).
+  - **Paired-end output**: Automatically splits into `_R1`, `_R2` files via `BuildPairedFileNames`.
+  - **Parallelism**: Uses configurable workers (`WriteParallelWorkers()`).
+  
+- **`BuildPairedFileNames(filename string) (string, string)`**  
+  Generates paired-end filenames: `sample.fastq → sample_R1.fastq`, `sample_R2.fastq`.
+
+## Configuration & Integration
+
+- **`OptionSet(allow_paired bool)`**  
+  Centralized CLI option setter. Enables modular setup for paired-end support and shared flags.
+
+- **Taxonomy Integration**:  
+  Supports loading taxonomy via `obioptions.LoadTaxonomyOptionSet`.
+
+- **Progress Reporting**:  
+  Displays a progress bar unless stderr is redirected or stdout pipes to another process.
+
+## Design Principles
+
+✅ Lazy evaluation via iterators for memory efficiency  
+✅ Automatic format inference and parallel I/O scaling  
+✅ Symlink resolution, recursive globbing with extension filtering  
+✅ CLI-integrated configuration (header parsing mode, workers, batch size)  
+
+All functionality is exposed through public functions and designed for composability with `obiformats`, `obiiter`, and `obidefault`.