Allow reading zipfile list from a file.

Android build generates 180K+ zip files that are to be merged and the
result passed to the indexing pipeline to generate the source code
cross-reference. Their names cannot be passed on the command line,
hence the need for this change. That required extensive changes to
the code as it no longer can be assumed that all the input files can
be kept open.

Bug: 121267023
Test: internal + treehugger + combine index files
Change-Id: I0a829f96ff7187ad967fb6b8cede387501ec57cc