⬆️ 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

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+# 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

autodoc/docmd/pkg/obioptions/subcommand.md

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+# Semantic Description of `GenerateSubcommandParser`
+
+The function `GenerateSubcommandParser` constructs a command-line argument parser with support for **subcommands**, leveraging the `go-getoptions` library.
+
+- It accepts:
+  - `program`: The program name (used for help/version).
+  - `documentation`: A top-level description of the tool.
+  - `setup`: A callback to register subcommands and their options.
+
+- Internally:
+  - Initializes a `GetOpt` instance with bundling mode (`-abc`) and strict unknown-option handling.
+  - Registers **global options** (e.g., `--debug`, `--verbose`) that are inherited by all subcommands.
+  - Invokes the user-provided `setup` function to define **subcommand-specific options and commands**.
+  - Automatically adds a built-in `help` subcommand for command-level documentation.
+
+- Returns:
+  - The root `*GetOpt`, required to invoke `.Dispatch()`.
+  - An `ArgumentParser` function (signature: `func([]string) (*GetOpt, []string)`), which:
+    - Parses command-line arguments (skipping `args[0]`, typically the binary name),
+    - Handles errors via `ProcessParsedOptions`,
+    - Returns parsed state and remaining positional arguments.
+
+This design enables a clean, hierarchical CLI structure: global flags → subcommands → per-command options/positional args.

autodoc/docmd/pkg/obioptions/version.md

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+# OBIOptions Package – Semantic Description
+
+The `obioptions` package provides a lightweight, version-aware utility for the OBITools suite. Its core functionality is centered around exposing runtime version information in a standardized and programmatic way.
+
+## Key Features
+
+- **Version Exposure**:  
+  Exposes the current version of OBITools via a simple, read-only function `VersionString()`. This allows other modules or external tools to query the package version at runtime.
+
+- **Automated Versioning**:  
+  The `_Version` variable is automatically populated from an external `version.txt` file during the build process (via Makefile), ensuring consistency between source metadata and compiled artifacts.
+
+- **Patch-Level Tracking**:  
+  The version follows semantic conventions (`MAJOR.MINOR.PATCH`), with the patch number incremented automatically on each repository push—enabling precise tracking of development iterations.
+
+- **No Side Effects**:  
+  The `VersionString()` function is pure: it takes no parameters and performs only a string return, making it safe for use in logging, diagnostics, or compatibility checks.
+
+- **Documentation Ready**:  
+  Includes inline GoDoc comments for clarity and tooling support (e.g., `go doc`), improving maintainability.
+
+## Use Cases
+
+- Debugging and logging (e.g., including version in error reports).  
+- Conditional logic based on OBITools compatibility.  
+- CI/CD validation (e.g., verifying deployed version matches expectations).  
+
+## Version Format
+
+`"Release X.Y.Z"` (e.g., `"Release 4.4.29"`), where:
+- `X` = Major release (breaking changes),
+- `Y` = Minor release (new features, backward-compatible),
+- `Z` = Patch level (incremented per push for hotfixes/bug fixes).
+
+No external dependencies or configuration required.