plex create deprecated

[acashmoney]

Includes refactors to plex init

The new 'hello-world' check which can be used is ./plex init -t tools/colabfold-mini.json -i '{"sequence": ["testdata/folding/test.fasta"]}' --scatteringMethod=dotProduct --autoRun=true -a test

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Based on the provided details of the Pull Request, here's a non-technical summary:

• Changes in Workflow Command Usage
  The relevant commands used in our workflow files have been updated. We've switched from using 'plex create' to 'plex init' and adjusted flags according to new requirements, improving command accuracy and flexibility. We also resolved an issue with an incomplete command, increasing overall system stability.

• Refactoring of 'create.go' to 'init.go'
  We decided to remove the "create.go" file and transferred its associated flags and functionalities to the "init.go" file. This activity simplifies our command structure and makes our code easier to maintain.

• Codebase Restructuring and Refactoring
  Various changes have been made throughout our frontend code, including changes to reducers, state management, logic changes, and fundamental structural alterations. These changes improve the efficiency of our code and the overall performance of our application.

• Infrastructure and Installation Changes
  We've updated a few of our scripts related to deployment and testing as well, migrating from the 'plex create' command to 'plex init' to align all functionalities following the refactoring.

• Internal Engineering Changes
  We've removed a few older or redundant code files and added new ones to better organize our codebase. This keeps our system lean, up-to-date, and efficient.

These changes all contribute to a more efficient, user-friendly, and maintainable system. However, these improvements are mostly under-the-hood and might not cause noticeable changes for the end-users but certainly improves the system's long-term viability and easiness in maintenance.

Gateway-specific changes included

• Ignoring 'gateway/gorm.db' in Version Control
  We've updated our ".gitignore" file to avoid tracking a database file. This reduces unnecessary noise in our version control system and keeps our codebase clean.

• Updates in Gateway Frontend
  New features and functionalities have been added to our app interface, including a job initialization and job viewing pages as well as data file listing implementation. This will provide our users with a richer, more interactive experience as they navigate our application.

[linear]

LAB-571 refactor `initializeIO`

Current version of initializeIO is large and difficult to debug, which adds problems to implementing similar functionality in the gateway. The purpose of this ticket is to refactor this, potentially also placing it into the ipwl package directly instead of living directly in init.go

[vercel]

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