General CLI fixes when building clikt executable

[btmonier]

Summary

This PR refactors the orchestration pipeline to use direct Clikt command invocations instead of spawning Gradle subprocesses, along with various bug fixes and improvements to CLI parameter handling.

Features

• Replaced all ProcessRunner.runCommand("./gradlew", "run", ...) calls with direct Clikt command parsing via CommandName().parse(args). This eliminates the overhead of spawning new Gradle/JVM processes for each pipeline step.
• Added restoreOrchestratorLogging() to maintain proper log file separation after each step runs.
• All paths are now resolved to absolute, normalized paths for consistency. This prevents issues with relative path resolution when working directories change.
• Changed config section parsing from map?.let { ... } to if (configMap.containsKey(...)) pattern. This allows pipeline steps to run with defaults even when config section is empty/null (i.e., just specifying the key enables the step).
• Added missing parameter features in downsample_gvcf and covert_to_fasta steps.
• General "QoL" updates to example pipeline YAML file.

Bug Fixes

• Fixed biokotlin-tools gzip naming (biokotlin-tools automatically compresses output and adds .gz extension)
• Temporary directories are now always cleaned up if they exist, not just when files were actively used from them.
• Added cleanup of ALL existing file appenders when setting up a new log file
• Prevents log bleeding where messages from step $N + 1$ appear in step $N$'s log file
• Properly stops old appenders before removing them
• Corrected binary name issue where "biokotlin" was called instead of "biokotlin-tools"

Breaking Changes

• None

Checklist

• I have updated the version in build.gradle.kts (REQUIRED - see below)
• I have tested these changes locally
• I have added/updated tests for new functionality
• I have updated documentation (if applicable)
• Breaking changes are clearly documented above

[zrm22]

Should this have 2 underscores at the end so it matches ignore_contig?

[btmonier]

Updated