sig describe and sig summarize differ on zip files with duplicate manifest entries

[ctb]

per #2748 (comment),

if you do something simple like run sketch twice to the same output file zip:

sourmash sketch dna fastq/0.fa -o 0.zip
sourmash sketch dna fastq/0.fa -o 0.zip

you will get different results from summarize and describe: summarize shows 2,

% sourmash sig summarize 0.zip

== This is sourmash version 4.8.4.dev0. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

** loading from '0.zip'
path filetype: ZipFileLinearIndex
location: /home/ctbrown/2023-ccbaumler-debug/0.zip
is database? yes
has manifest? yes
num signatures: 2
** examining manifest...
total hashes: 8336
summary of sketches:
   2 sketches with DNA, k=31, scaled=1000             8336 total hashes

but describe only shows 1:

% sourmash sig describe 0.zip

== This is sourmash version 4.8.4.dev0. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

---
signature filename: /home/ctbrown/2023-ccbaumler-debug/0.zip
signature: ** no name **
source file: fastq/0.fa
md5: 324074c7287ed934af4fd0a6a459aa30
k=31 molecule=DNA num=0 scaled=1000 seed=42 track_abundance=0
size: 4168
sum hashes: 4168
signature license: CC0

loaded 1 signatures total, from 1 files

There is indeed only one sketch in the zip file,

unzip -v 0.zip 
Archive:  0.zip
 Length   Method    Size  Cmpr    Date    Time   CRC-32   Name
--------  ------  ------- ---- ---------- ----- --------  ----
   34804  Stored    34804   0% 2023-09-22 06:27 e5e9328b  signatures/324074c7287ed934af4fd0a6a459aa30.sig.gz
     386  Stored      386   0% 2023-09-22 06:27 b9dbdae2  SOURMASH-MANIFEST.csv
--------          -------  ---                            -------
   35190            35190   0%                            2 files

but there are two entries in the manifest:

% cat SOURMASH-MANIFEST.csv 
# SOURMASH-MANIFEST-VERSION: 1.0
internal_location,md5,md5short,ksize,moltype,num,scaled,n_hashes,with_abundance,name,filename
signatures/324074c7287ed934af4fd0a6a459aa30.sig.gz,324074c7287ed934af4fd0a6a459aa30,324074c7,31,DNA,0,1000,4168,False,,fastq/0.fa
signatures/324074c7287ed934af4fd0a6a459aa30.sig.gz,324074c7287ed934af4fd0a6a459aa30,324074c7,31,DNA,0,1000,4168,0,,fastq/0.fa

so this looks like another case of slightly pathological manifest misrepresentation, sigh.

It is weird to me that the zip file saving code is ADDING a manifest entry but NOT adding a second signature file too 😭

cc #2749 #1849 #1837