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

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

2. You don’t 🙃

/s Sorry, I had to 🤣

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.

I see syncthing; I comment this.

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/

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’.