The entire contents of your packaged app are available to both JavaScript and NaCl code via http requests.
If you use the nacl_io library then you can also access all the files using standard POSIX file APIs by first mounting the contents of the package somewhere if your virtual filesystem:
e.g:
// Mount the http root at /mnt/package/
mount("/", "/mnt/package/", "httpfs", 0, "");
FILE* f = fopen("/mnt/package/somefile", "r");