Is there a command line molecular cloning tool?
Making maps of plasmids Annotating plasmids with common features


Plasmapper works through commandline


  Finding restriction sites


Simple regex searches can do that


  Mapping Sanger sequencing reads


BLAST will do it. 


  Showing sequence, reverse complement of the sequence, translations in
  different frames 


EMBOSS has a collection of tools for these things. (getorf is a tool for finding ORFs)


  Designing primers for specific applications (such as
  Gibson cloning)


Primer3 works through commandline




You can just download the entire EMBOSS collection. It has many useful tools.