All extensions, even Pop ones, disabled after updating with apt and flatpak

Distribution (run cat /etc/os-release):

NAME="Pop!_OS"
VERSION="22.04 LTS"
ID=pop
ID_LIKE="ubuntu debian"
PRETTY_NAME="Pop!_OS 22.04 LTS"
VERSION_ID="22.04"
HOME_URL="https://pop.system76.com"
SUPPORT_URL="https://support.system76.com"
BUG_REPORT_URL="https://github.com/pop-os/pop/issues"
PRIVACY_POLICY_URL="https://system76.com/privacy"
VERSION_CODENAME=jammy
UBUNTU_CODENAME=jammy
LOGO=distributor-logo-pop-os

Related Application and/or Package Version (run apt policy $PACKAGE NAME):

gnome-extensions-app

Issue/Bug Description:

After some upgrades (not sure exactly which just yet), I am unable to activate any extensions even Pop!_OS ones like Pop Shell.
I'm not sure if it is related by alt+f2 and r and enter no longer restarts Gnome shell. It returns "Command not found"...
Even using control and the arrow keys doesn't move the cursor by words anymore...

Steps to reproduce (if you know):

Keep your machine up-to-date by running sudo apt update && sudo apt upgrade && flatpak update.
Eventually, this happens.

Expected behavior:

Updating my computer doesn't remove relied upon and key functionality.

Other Notes:

             /////////////                davidrhoderick@davidrhoderick-amddesktop 
         /////////////////////            ---------------------------------------- 
      ///////*767////////////////         OS: Pop!_OS 22.04 LTS x86_64 
    //////7676767676*//////////////       Host: X570 I AORUS PRO WIFI -CF 
   /////76767//7676767//////////////      Kernel: 6.8.0-76060800daily20240311-generic 
  /////767676///*76767///////////////     Uptime: 5 mins 
 ///////767676///76767.///7676*///////    Packages: 2214 (dpkg), 8 (brew), 41 (flatpak), 7 (snap) 
/////////767676//76767///767676////////   Shell: fish 3.7.1 
//////////76767676767////76767/////////   Resolution: 3840x2160, 3840x2160 
///////////76767676//////7676//////////   DE: GNOME 42.9 
////////////,7676,///////767///////////   WM: Mutter 
/////////////*7676///////76////////////   WM Theme: Adwaita 
///////////////7676////////////////////   Theme: Pop-dark [GTK2/3] 
 ///////////////7676///767////////////    Icons: Pop [GTK2/3] 
  //////////////////////'////////////     Terminal: tilix 
   //////.7676767676767676767,//////      CPU: AMD Ryzen 7 PRO 4750G with Radeon Graphics (16) @ 4.454GHz 
    /////767676767676767676767/////       GPU: AMD ATI 0a:00.0 Renoir 
      ///////////////////////////         Memory: 9772MiB / 63682MiB 
         /////////////////////
             /////////////

I made a reddit post here too.

pop-os / pop

All extensions, even Pop ones, disabled after updating with apt and flatpak #3288