The appropriate directory's are the XDG Base Directory, check this page on arch wiki to move them correctly. You can also use xdg-ninja and it will scan for these extra directories on your $HOME and tell you what you need to do to move them to their appropriate location or not if these directories are hardcoded or cannot be moved.

~/go is created when compiling go programs, you can change it's location with the GOPATH environment variable to something like GOPATH=$HOME/.local/go, and moving the directory there.

Never seen ~/perl5, could you provide the output of perl -V

I don't like the mess some software makes when it install in my system

I gave up bothering about this a decade ago and I just store my files elsewhere while software treat the home directory as 'application data'.

Don't know about perl but for go you need to look up setting gopath like here https://stackoverflow.com/questions/10838469/how-to-compile-go-program-consisting-of-multiple-files/61793820#61793820

RE Go: Others have already mentioned the right way, thought I'd personally prefer ~/opt/go over what was suggested.

RE Perl: To instruct Perl to install to another directory, for example to ~/opt/perl5, put the following lines somewhere in your bash init files.

export PERL5LIB="$HOME/opt/perl5/lib/perl5${PERL5LIB:+:${PERL5LIB}}"
export PERL_LOCAL_LIB_ROOT="$HOME/opt/perl5${PERL_LOCAL_LIB_ROOT:+:${PERL_LOCAL_LIB_ROOT}}"
export PERL_MB_OPT="--install_base \"$HOME/opt/perl5\""
export PERL_MM_OPT="INSTALL_BASE=$HOME/opt/perl5"
export PATH="$HOME/opt/perl5/bin${PATH:+:${PATH}}"

Though you need to re-install the Perl packages you had previously installed.

2. You don't 🙃

/s Sorry, I had to 🤣

I see syncthing; I comment this.

Try xdg-ninja to learn how to move them (and everything else) away from your home directory.

1. usually ~/.config/PROGRAM_NAME/

You probably want to look into $XDG_CONFIG_HOME and the freedesktop spec documentation if you are interested in more of where these standards come from:
https://specifications.freedesktop.org/basedir-spec/latest/ar01s02.html

(and more generally)

https://www.freedesktop.org/wiki/Specifications/