Add set_execution_mode param and UDOCKER_SET_EXECUTION_MODE to for udocker run

[gaberudy]

New Feature: Automatic Execution Mode Setting

This PR adds a new configuration parameter set_execution_mode and environment variable UDOCKER_SET_EXECUTION_MODE that allows automatic setting of execution mode when running containers from images.

What it does

When UDOCKER_SET_EXECUTION_MODE is set, udocker will automatically create a container and set the execution mode before running when using udocker run with an image name. This eliminates the need for manual container creation and execution mode setup.

Example Usage

Before (manual approach):

udocker create --name=hiphase quay.io/pacbio/hiphase:1.5.0_build1
udocker setup --execmode=F3 hiphase
udocker run hiphase hiphase --help

After (automatic approach):

export UDOCKER_SET_EXECUTION_MODE=F3
udocker run quay.io/pacbio/hiphase:1.5.0_build1 hiphase --help

Configuration Options

The feature can be configured in two ways:

1. Environment variable:

   export UDOCKER_SET_EXECUTION_MODE=F3

2. Configuration file (~/.udocker/udocker.conf):

   set_execution_mode = F3

Documentation Updates

• Updated CHANGELOG.md with version 1.3.18 entry
• Added documentation to docs/installation_manual.md
• Added documentation to docs/reference_card.md
• Added documentation to docs/user_manual.md

This feature is particularly useful for users who use tools like miniwdl that invoke udocker run with a image:tag, but need to specify specific execution modes and do not have an option to use the create + setup + run strategy.