Refactor most "cg store" commands to be called "cg prepare"

[mogmi]

Description

Proposed changes for the commands currently named cg store to be renamed to avoid confusion with the cg workflow <workflow> store. The purpose of the command is (mostly) to make decompressed Fastq files available for analysis by updating Housekeeper. My suggestion for the new name is prepare because:

• Not all files are FASTQs ( demultiplexed-run includes all bundle files)
• The command never starts decompression — so "decompress" would be misleading
• "link" already means filesystem linking in other cg commands, not Housekeeper registration
• "ingest" implies raw data, but the files are already compressed/demultiplexed in the system
• "stage" conflicts with the staging environment terminology used by the team
• "prepare" might be to general but at least covers the shared intent: making files ready for analysis, regardless of the specific mechanism

But the name needs to be discussed - this PR is just to illustrate what changes are needed, less than I anticipated.

cg store qc-metrics is left untouched since it has a very different purpose from the others

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud