I accidentally scrambled all the permissions on my home directory by running sudo chmod -R -755 .

The -R does this recursively through out every sub directory under /home/user/

While this looks somewhat innocent and harmless, most (if not all) files on home directory are owned by normal user. The above command just changed all files ownership to root (privileged user) which has alot of nuisance.

Effects:

1. To run any app now, you need to open a new terminal and type sudo -E app-name &, every single time. Annoying, but not as much as the following effects...
2. Running apps this way is not recommended since the app might accidentally change your system configurations without remorse, as it's launched with root privileges (eg. network sockets, of which might most certainly be used by another app or daemon) and lead into hundreds of popups telling you that some system app terminated unexpectedly (without any reason whatsoever! Now you have to hunt that reason out on dmesg or sm'n). This can and WILL certainly lead to Linux crashes.
3. Due to effects on 2. Above, most apps (eg. Android studio) WILL prevent you from launching it with root privileges, by quiting itself immediately when it detects that privileged user is owner of the application process. So you will wind up with apps that you might never use again 😕

It's a world pain by a thousand tinny cuts.

Hope this answers all your questions, and yes, it's -R, not -r

Solutions:

1. Be extra extra careful while running sudo commands, especially those with -R (recursive) options. Are you on a right directory? ( I thought I was, turns out I wasn't)

in addition to above, I would try to avoid using ., and specify the particular directory using ~/path/to/dir. So, instead of sudo chmod -R -755 ., I could have used sudo chmod -R -755 ~/path/to/dir

2. timeshift to the rescue. Backup your home directory (except Downloads and Video folders), preferably weekly, (or daily if you change your system configurations more frequently)