You may also check the repository/fs2mod file adding logic : I can add empty stuff in there, and that leaves blank spaces in the sources list.
A lot of these bugs look awfully similar to the bugs I encountered with the bash version (wrong path forcing full re-download, adding empty stuff to the cache...)

Also, we're lucky that Dropbox keeps copies of old revisions, because (Ireally don't know how) Derelict.fs2mod was replaced by an empty text file using the same name, 2 times. Any idea what could be causing that ? (maybe it had something to do with adding and deleting empty repositories and it's fixed already ?)
(I'm not sure why, but when a fs2mod file is added, it's also always rewritten. Looks unsafe to me)
Each time I switch between launching the installer with python2 and python3, it loses all its cache and settings, and ends up doing all checksums again on next launch. Is it possible to avoid the issue ?
"#!/usr/bin/python3" may be necessary in Ubuntu, since it defaults to python2 if we directly launch the script.
The desktop entry alone doesn't work, it also needs to be referenced in "~/.local/share/applications/mimeapps.list"
[Desktop Entry]
Name=fs2mod-py
Exec=python3 /home/loris/fs2mod-py-develop/manager.py %U
Icon=/home/loris/fs2mod-py-develop/hlp.png
Type=Application
Terminal=false
MimeType=x-scheme-handler/fso;
Append this to "~/.local/share/applications/mimeapps.list"
x-scheme-handler/fso=fs2mod-py.desktop;
Something else : secondary progress bars appear in python3, not in python2. The main progress bar is ok in both.
I am also experiencing priority issues between the HLP repository and fs2mod files. Not sure which priority is intended behaviour.
(how complicated would it be to allow reordering of sources in the settings tab ?)
If I try to launch a mod from manager.py, fso currently crashes. I heard parsing flags and tabbed settings for fs2_open is not something easy. You could be interested in wxLauncher source code. I'm not sure what is your intention about launching mods directly from the mod installer (something like a "light" launcher ?)
Currently, wxLauncher is "profile centric" : it can store different settings profiles, with basic options, advanced options, and mod settings, for each profile.
A one-click mod install/launch process would need a "mod centric" launcher : base settings (screen resolution, AA, AF, controller, sound device) should be shared between all mods, while advanced settings (especially lighting, hud features...) should be set separately for each mod. When you chose to launch a mod, right settings are selected. wxLauncher has no way to that currently, and implementing it would end up with a bloated code base.
Something like fso://settings (for default profile, the one which is copied for default settings when we start a new mod for the first time) and fso://settings/Derelict (for Derelict profile) link to bring up a really simple settings screen would be great, with only the base settings, and a button to access a text zone to enter advanced flags (a bit like what steam does).