Both Pan and Kitchen can pull PDI content files from out of Zip files. To do this, use the ! switch, as in this example:
Kitchen.bat /file:"zip:file:///C:/Pentaho/PDI Examples/Sandbox/linked_executable_job_and_transform.zip!Hourly_Stats_Job_Unix.kjb"
If you are using Linux or Solaris, the ! must be escaped:
./kitchen.sh -file:"zip:file:////home/user/pentaho/pdi-ee/my_package/linked_executable_job_and_transform.zip\!Hourly_Stats_Job_Unix.kjb"