The problem with regular zip is that the zip archive contains a “mimetype” file that shouldn’t be compressed if you want InDesign to identify the newly-created IDML. So the way you have to re-zip the file (and the way the ePub scripts work) is like this:
They first create a zip archive which contains only the mimetype file, uncompressed. zip -X0 'myfile.idml' mimetype
Then they add the rest of the files/folders into the zip archive, this time with full compression. zip -rDX9 "myfile.idml" * -x "*.DS_Store" -x mimetype
In shell script terms, the ePub scripts do this (assuming the current directory is the one containing all the IDML contents):
zip -X0 'myfile.idml' mimetype
# create the zip archive 'myfile.idml', containing only the 'mimetype' file with no compression
zip -rDX9 "myfile.idml" * -x "*.DS_Store" -x mimetype
# add everything else to the ‘myfile.idml’ archive, EXCEPT .DS_Store files and the ‘mimetype’ file (which is already there from the previous step)
To save you time reading the zip man page, here’s what all these options mean:
-X
= “no extra” — do not save extra file attributes like user/group ID for each file
-0
= “compression level zero” — no compression
-r
= “recurse paths” — go through everything in the directory, including nested subfolders
-D
= “no directory entries” — don’t put special stuff in the zip archive for directories
-9
= “compression level 9 (optimal)”
-x
= “exclude these files”
Follow this voodoo, and you should be able to create legal IDML files.
Source: http://indesignsecrets.com/topic/how-do-i-re-zipcompress-an-expanded-idml-file
A big thanks to Chuck Weger and David Blatner at http://indesignsecrets.com