On debian stretch I observe that apt-file udpate (which on stretch
just calls apt update) does not download the Contents-<arch> index files at all
in case of using an aptly-created mirror. When using an official debian
mirror, it immediately works just fine.

Detailed Description

(I reviewed the already fixed bug report #667 and that seems not to be the same issue as described here.)

I was able to confirm that those Contents files indeed exist in my published
snapshot of a debian mirror and are also listed in the Release / InRelease files
with correct hashes. However when I compared the InRelease file of an official
debian mirror with the one of my aptly mirror, I recognized this difference:

my published aptly mirror:

78156fa4c3dc2d9738baeeb4910d6dc4    31931 main/Contents-amd64.gz

official mirror:

 71ffc92735ac8621dc4bface380b8311 455005144 main/Contents-amd64
 000fc46f21ad2c46d1affa5f8e829527 31399649 main/Contents-amd64.gz

So the official mirror also lists the hash of the uncompressed Contents file,
but the aptly mirror does not. On both the official mirror and my aptly mirror,
the actual uncompressed file Contents-amd64 does not exist, just the compressed
Contents-amd64.gz exists (as it should be, to my understanding).

For other index files like Packages, the file InRelease of my aptly mirror
contains both hashes for compressed and uncompressed file, just for Contents
files it is different. Why? Might this be the problem? Or did I misinterpret
stuff?

The debian wiki says about that:

"The checksum and sizes shall match the actual existing files. If indexes are
compressed, checksum data must be provided for uncompressed files as well, even
if not present on the server."

On debian jessie I do not get problems like that. There apt-file update was
implemented differently (not using apt update in behind... one can easily
see this because on jessie it shows progress output of curl, and on stretch
the output looks completely different).

Your Environment

I am using aptly 1.3.0 (and also tried the latest nightly build 1.3.0+17+g9a704de with the same result).