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I'm using rxvt-unicode for it's the less flawed terminal emulator I know.

I'm looking for using Ctrl + Arrow keys and Home / End to navigate through command line text, to emulate the behavior of all other modern text fields.

Could anyone help me solve this issue?

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Something else is eating your keys, the window manager most likely. Go to settings and set virtual desktop switching to something else.

The behavior you are describing is the default (readline commands).

$ bind -p| grep -E 'forward|backward-word' |grep -v "^#"
"\e\e[D": backward-word
"\eOd": backward-word
"\e[1;3D": backward-word
"\e[1;5D": backward-word           #<---- this
"\e[5D": backward-word
"\eb": backward-word
"\C-f": forward-char
"\eOC": forward-char
"\e[C": forward-char
"\C-s": forward-search-history
"\e\e[C": forward-word
"\eOc": forward-word
"\e[1;3C": forward-word
"\e[1;5C": forward-word            #<----- and here
"\e[5C": forward-word
"\ef": forward-word
"\e[6~": history-search-forward
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