big shellcheck cleanup and disabling the shellchecks we will ignore

lib/apply_CHANGES.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+# shellcheck disable=SC1091
 
 function make_BACKUP () {
     local BACKUPDIR
@@ -127,7 +128,7 @@ unless a backup already exist.
 Then the files above will be copied to your system followed by running followed by updating your
 initramfs and then attempt adding new kernel arguments to your bootloader."
 	
-	read -p "Do you want to proceed with the installation of the files? (no=quit) [Y/n]: " YESNO
+	read -r -p "Do you want to proceed with the installation of the files? (no=quit) [Y/n]: " YESNO
 
     case "${YESNO}" in
         [Nn]*)

lib/get_GPU_GROUP.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+# shellcheck disable=SC1091
 
 function get_GPU_GROUP () {
     clear

lib/get_GPU_ROM.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+# shellcheck disable=SC1091,SC2024
 
 function get_GPU_ROM () {
     clear

lib/get_USB_CTL_GROUP.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+# shellcheck disable=SC1091
 
 function get_USB_CTL_GROUP () {
     clear
@@ -26,7 +27,7 @@ To return to the previous page just press ENTER.
         [Yy]*)
             # Get the PCI ids
             local PCI_ID
-            PCI_ID=$($SCRIPTDIR/utils/ls-iommu | grep -i "group $1" | cut -d " " -f 4 | perl -pe "s/([0-9a-f]{2}:[0-9a-f]{2}.[0-9a-f]{1})\n/\"\1\" /" | perl -pe "s/\s$//")
+            PCI_ID=$("$SCRIPTDIR/utils/ls-iommu" | grep -i "group $1" | cut -d " " -f 4 | perl -pe "s/([0-9a-f]{2}:[0-9a-f]{2}.[0-9a-f]{1})\n/\"\1\" /" | perl -pe "s/\s$//")
 
             # Replace the blank USB_CTL_ID with the PCI_ID for the usb controller the user wants to pass through
             perl -pi -e "s/USB_CTL_ID=\(\)/USB_CTL_ID=\($PCI_ID\)/" "$SCRIPTDIR/$QUICKEMU/qemu-vfio_vars.conf"

lib/paths.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+# shellcheck disable=SC2034
 MODPROBE="config/etc/modprobe.d"
 INITRAMFS="config/etc/initramfs-tools"
 ETCMODULES="config/etc/modules"

lib/set_CMDLINE.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+# shellcheck disable=SC1091
 
 # Function to configure systemd-boot using kernelstub
 function set_KERNELSTUB () {
@@ -51,13 +52,13 @@ function set_GRUB () {
     if grep -q "GRUB_CMDLINE_LINUX_DEFAULT=" "$SCRIPTDIR/$DEFAULT/grub" ;
     then
         # Update the GRUB_CMDLINE_LINUX_DEFAULT line
-        GRUB_CMDLINE=$(cat "/etc/default/grub" | grep -P "^GRUB_CMDLINE_LINUX_DEFAULT" | perl -pe "s/GRUB_CMDLINE_LINUX_DEFAULT=\"(.+)\"/\1/" | perl -pe "s/iommu=(pt|on)|amd_iommu=on|vfio_pci.ids=.+|vfio_pci.disable_vga=\d{1}//g" | perl -pe "s/(^\s+|\s+$)//g")
+        GRUB_CMDLINE=$(grep -P "^GRUB_CMDLINE_LINUX_DEFAULT" "/etc/default/grub" | perl -pe "s/GRUB_CMDLINE_LINUX_DEFAULT=\"(.+)\"/\1/" | perl -pe "s/iommu=(pt|on)|amd_iommu=on|vfio_pci.ids=.+|vfio_pci.disable_vga=\d{1}//g" | perl -pe "s/(^\s+|\s+$)//g")
-        GRUB_CMDLINE_LINUX=$(cat "/etc/default/grub" | grep -P "^GRUB_CMDLINE_LINUX_DEFAULT")
+        GRUB_CMDLINE_LINUX=$(grep -P "^GRUB_CMDLINE_LINUX_DEFAULT" "/etc/default/grub")
         perl -pi -e "s/${GRUB_CMDLINE_LINUX}/GRUB_CMDLINE_LINUX_DEFAULT=\"${GRUB_CMDLINE} ${CMDLINE}\"/" "${SCRIPTDIR}/$DEFAULT/grub"
     else
         # Update the GRUB_CMDLINE_LINUX line
-        GRUB_CMDLINE=$(cat "/etc/default/grub" | grep -P "^GRUB_CMDLINE_LINUX" | perl -pe "s/GRUB_CMDLINE_LINUX=\"(.+)\"/\1/" | perl -pe "s/iommu=(pt|on)|amd_iommu=on|vfio_pci.ids=.+|vfio_pci.disable_vga=\d{1}//g" | perl -pe "s/(^\s+|\s+$)//g")
+        GRUB_CMDLINE=$(grep -P "^GRUB_CMDLINE_LINUX" "/etc/default/grub" | perl -pe "s/GRUB_CMDLINE_LINUX=\"(.+)\"/\1/" | perl -pe "s/iommu=(pt|on)|amd_iommu=on|vfio_pci.ids=.+|vfio_pci.disable_vga=\d{1}//g" | perl -pe "s/(^\s+|\s+$)//g")
-        GRUB_CMDLINE_LINUX=$(cat "/etc/default/grub" | grep -P "^GRUB_CMDLINE_LINUX")
+        GRUB_CMDLINE_LINUX=$(grep -P "^GRUB_CMDLINE_LINUX" "/etc/default/grub")
         perl -pi -e "s/${GRUB_CMDLINE_LINUX}/GRUB_CMDLINE_LINUX=\"${GRUB_CMDLINE} ${CMDLINE}\"/" "${SCRIPTDIR}/$DEFAULT/grub"
     fi
     

lib/set_DRACUT.sh

@@ -1,4 +1,6 @@
 #!/bin/bash
+# shellcheck disable=SC1091
+
 function set_DRACUT () {
     # Get the config paths
     source "$SCRIPTDIR/lib/paths.sh"

lib/set_INITRAMFSTOOLS.sh

@@ -1,12 +1,13 @@
 #!/bin/bash
+# shellcheck disable=SC1091
 
 function insert_INITRAMFSTOOLS() {
     # Get the header and enabled modules separately from the /etc/modules file
     local MODULES_HEADER
     local MODULES_ENABLED
     local VENDOR_RESET
-    MODULES_HEADER=$(head -n $1 "$2" | grep -P "^#" | grep -v "# Added by quickpassthrough")
+    MODULES_HEADER=$(head -n "$1" "$2" | grep -P "^#" | grep -v "# Added by quickpassthrough")
-    MODULES_ENABLED=$(cat "$2" | grep -vP "^#" | grep -v "vendor-reset")
+    MODULES_ENABLED=$(grep -vP "^#" "$2" | grep -v "vendor-reset" | perl  -pe  "s/^\n//")
     VENDOR_RESET=0
     
     # If vendor-reset is present

lib/set_MKINITCPIO.sh

@@ -1,4 +1,6 @@
 #!/bin/bash
+# shellcheck disable=SC1091
+
 function set_MKINITCPIO () {
     # Get the config paths
     source "$SCRIPTDIR/lib/paths.sh"

lib/set_MODPROBE.sh

@@ -1,4 +1,6 @@
 #!/bin/bash
+# shellcheck disable=SC1091
+
 function set_MODPROBE () {
     # Get the config paths
     source "$SCRIPTDIR/lib/paths.sh"

lib/set_VFIO.sh

@@ -1,4 +1,6 @@
 #!/bin/bash
+# shellcheck disable=SC1091
+
 function set_VFIO () {
     # Get the config paths
     source "$SCRIPTDIR/lib/paths.sh"

vfio-setup

@@ -1,14 +1,15 @@
 #!/bin/bash
+# shellcheck disable=SC1091
 
 # Get the scripts directory
 SCRIPTDIR=$(dirname "$(realpath "$0")")
-cd "$SCRIPTDIR"
+cd "$SCRIPTDIR" || exit
 
 # Get the config paths
 source "$SCRIPTDIR/lib/paths.sh"
 
 # Get the CPU Vendor
-CPU_VENDOR=$(cat /proc/cpuinfo | grep vendor | head -1 | cut -f 2 | cut -d " " -f 2)
+CPU_VENDOR=$(grep "vendor_id" /proc/cpuinfo | head -1 | cut -f 2 | cut -d " " -f 2)
 CMDLINE="iommu=pt"
 
 # Adjust our kernel_args based on cpu vendor

vfio-verify

@@ -1,18 +1,19 @@
 #!/bin/bash
+# shellcheck disable=SC2002,SC2164
 
 # Get the scripts directory
-SCRIPTDIR=$(dirname "$(which $0)")
+SCRIPTDIR=$(dirname "$(which "$0")")
 cd "$SCRIPTDIR"
 
 # If there is a config generated, then $SCRIPTDIR/config/kernel_args
 # should exist, which contains all the info we need
-if [ -f $SCRIPTDIR/config/kernel_args ];
+if [ -f "$SCRIPTDIR/config/kernel_args" ];
 then
     # Fetch part of the device id we need
-    DEVID=$(cat $SCRIPTDIR/config/kernel_args | cut -d " " -f 3 | cut -d "=" -f 2 | perl -pe "s/^([0-9a-f]{4}:).*/\1/")
+    DEVID=$(cat "$SCRIPTDIR/config/kernel_args" | cut -d " " -f 3 | cut -d "=" -f 2 | perl -pe "s/^([0-9a-f]{4}:).*/\1/")
     echo "#------------------------------------------#"
     # List info about the vfio gpu and what kernel driver is being used
-    lspci -d $DEVID -v | grep -iP "kernel driver|amd|radeon|nvidia|nouveau" | grep -vi "kernel modules"
+    lspci -d "$DEVID" -v | grep -iP "kernel driver|amd|radeon|nvidia|nouveau" | grep -vi "kernel modules"
     echo "#------------------------------------------#"
 
     printf "