#I screwed up.
Last year I wrote a guide about how to install Nemo (with minimal files and dependencies). This advice is going to be included in a modified version, but as well, include why the problem happens in the first place.
#The problem
###Why is this (not) happening?
When using Webupd8's PPAs to install Nemo, there are some critical things that are excluded for Nemo to function fully. Namely, the dconf schemas to handle how media is used. Disks don't mount, nothing works automatically, even after you screw around in dconf-editor, and this is because Nemo, as had been stated before is a desktop and file manager for Cinnamon.
###How I found out
While Nemo and Caja come from the same heritage, how the media handling stuff is done differs between the two. While in Caja all of the media handling stuff is there, in Nemo the Media tab was broken off into Cinnamon's Preferred Applications window. But these differences are more than skin-deep; Both file managers write these preferences to different dconf schemas. While looking in dconfeditor for both Ubuntu MATE and Linux Mint Cinnamon, I found out the schemas all this autorun stuff is written to;
MATE; org.mate.media-handling
Cinnamon; org.cinnamon.desktop.media-handling
And if Cinnamon looks familiar, then it's because it mimics this;
org.gnome.desktop.media-handling
Which is where I thought the resolution was. But horror of horrors, Webupd8's modified Nemo repos excludes the CInnamon schemas necessary for Nemo to run properly. They don't even fix it so it uses GNOME's schemas, which would had instantly resolved the issue then and there.
#The solution
###After following my guide
Don't do what I tell you. At least, sometimes. In my guide I had this bit of advice;
[quote]Still within the same terminal, do the following;
gsettings set org.mate.session.required_components filemanager 'nemo -n'
[/quote]
No. That is stupid if you want to keep your autorun stuff functional. I'll redact this piece of information in favor for the advice of hiding the desktop icons for caja via mate-tweak or gsettings and leaving it running.
Even though Caja will continue to be running in the background, Nemo will run on top of it. And since Nemo will be showing its own desktop icons, doing caja -q for any reason will not cause Caja to override the desktop icons.
###Installing Nemo normally
If you decline to use the PPAs and instead choose to install Nemo normally, it'll be an outdated version (as seen with apt-cache policy nemo but you have the option of Cinnamon's schemas, so you can transplant your autorun settings for Caja into Nemo by way of copying strings and arguments from org.mate.media-handling into org.cinnamon.desktop.media-handling. After, you can add the webupd8 PPA compatible for your system and receive the latest version, presumably while keeping all the schemas so you can get the best of both them and the newest Nemo... hopefully. Soon to be tested.