Merge conflicts resolved pr of v1.2

[ZLI-afk]

1. fix missing STRU from upload_dir & update README.md bac5c0d
2. inject phonolammps run command in single step run mode eb56616
3. change run subcommand name into do a7d270b

[codecov]

Codecov Report

Attention: Patch coverage is 11.11111% with 8 lines in your changes are missing coverage. Please review.

Project coverage is 59.65%. Comparing base (d11ec01) to head (cd8c79b).

Files	Patch %	Lines
apex/core/lib/dispatcher.py	16.66%	5 Missing ⚠️
apex/core/common_prop.py	0.00%	3 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff               @@
##           devel-1.2.0      #56      +/-   ##
===============================================
- Coverage        59.67%   59.65%   -0.03%     
===============================================
  Files               55       55              
  Lines             6239     6243       +4     
===============================================
+ Hits              3723     3724       +1     
- Misses            2516     2519       +3     

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[ZLI-afk]

All conflicts are resolved and ready to be merged.