⬆️ 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/obioptions/options.md

@@ -0,0 +1,47 @@
+# OBIOptions Package: Global Command-Line Interface Utilities
+
+The `obioptions` package provides shared command-line argument parsing and runtime configuration for OBITools4 commands. It centralizes common options, logging setup, profiling controls, and taxonomy handling.
+
+## Core Functionalities
+
+- **Global Option Registration**: `RegisterGlobalOptions()` defines shared flags such as:
+  - `--version`, `--debug`
+  - CPU/thread control (`--max-cpu`)
+  - Batch processing parameters: `--batch-size`, `-size-max`, `--batch-mem`
+  - Quality encoding (`--solexa`)
+  - Warning suppression (`--silent-warning`)
+
+- **Option Processing**: `ProcessParsedOptions()` handles post-parsing logic:
+  - Prints help/version and exits on request
+  - Loads default taxonomy via `obiformats.LoadTaxonomy()`
+  - Configures log level (debug/info)
+  - Starts `pprof` HTTP servers for performance profiling:
+    - Generic (`/debug/pprof`)
+    - Mutex contention (`--pprof-mutex`, `runtime.SetMutexProfileFraction()`)
+    - Goroutine blocking (`--pprof-goroutine`, `runtime.SetBlockProfileRate()`)
+
+- **Parser Generator**: `GenerateOptionParser()` builds a reusable argument parser with:
+  - Bundled short options (`-abc`)
+  - Strict unknown-option handling
+  - Automatic `--help` support
+
+## Taxonomy Integration
+
+- `LoadTaxonomyOptionSet()` registers taxonomy-specific flags:
+  - Required/optional path to DB (`--taxonomy`, `-t`)
+  - Alternative names search (`--alternative-names`)
+  - Taxonomic validation: `--fail-on-taxonomy`, automatic updates via `--update-taxid`
+  - Raw taxID output (`--raw-taxid`)
+  - Leaf sequences inclusion via `--with-leaves`
+
+## Runtime Accessors
+
+- `CLIIsDebugMode()`, `SeqAsTaxa()` → read current state
+- `SetDebugOn/Off()` → programmatic debug toggling
+
+## Design Principles
+
+- Environment variable support (`OBIMAXCPU`, `OBIWARNING`, etc.)
+- Thread-safe taxonomy loading with mutex
+- Graceful error handling (parse errors → help + exit)
+- Integration with `logrus` and Go’s standard profiling tools