Dump directories have sub-directories for each database. Inside each database directory there is a metadata.json file for each collection. This file contains an extJSON representation of the collection options and index definitions. You can edit this file in a text editor to change the options and indexes.
If the dump was created with the --gzip option, the metadata.json file will be compressed. It will be a metadata.json.gz file. You can uncompress the file, edit it, then recompress it.