Updated installation scripts and docker install. Fixed samplesheet parse and using application folder samba param

[saramonzon]

High-level summary

This PR introduces a set of improvements to the Docker runtime handling, database migrations workflow, installation scripts, Samba configuration, and documentation.
Closes #387

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Docker Runtime & Configuration

• Copy Docker runtime to tmp when path is outside the repository
• Copy Docker runtime into the repository when required for external paths
• Renamed docker-compose.yml to docker-compose.test.yml
• Fixed and improved passing of git revision to the Dockerfile
• Ensured configuration files are accessible from within the container
• Updated Docker test install settings name
• Switched IP to Docker internal networking for proper local execution
• Opened Docker network to allow connection to localhost MySQL (not required if MySQL is external)

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Installation & Scripts

• Applied multiple fixes in docker_install.sh
• Added comment in install.sh clarifying the second migrate command
• Fixed getopts handling for script-before option
• Added support for script-before and script-after migration hooks
• Fixed function not using application folder path correctly
• Fixed disk utilization check to correctly resolve application folder
• Removed --exclude migrations from rsync
• Reverted unintended change affecting behavior

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Database & Migrations

• Removed migrations from .gitignore
• Removed app-based .gitignore
• Committed baseline migration files
• Added new migrations for develop changes
• Dropped foreign key before removing run_process_id_id
• Added required export for library pool many-to-many relation
• Added developer notes on how to create migration files
• Added documentation describing migration scripts and related versions
• Updated upgrade scripts documentation with execution order information

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Samba Configuration

• Updated Samba configuration for test data
• Fixed shared folder resolution when Samba application folder is present in configuration

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Parsing & Application Fixes

• Fixed samplesheet parsing logic

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Documentation & Messaging

• Clarified documentation across README and related docs
• Improved user-facing messages
• General documentation improvements for clarity and consistency

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Related Issues

N/A

[Aberdur]

LGTM 🙌