Source: https://hex-rays.com/blog/igors-tip-of-the-week-33-idas-user-directory-idausr/

$IDAUSR / %IDAUSR%

• On Windows: %APPDATA%/Hex-Rays/IDA Pro
• On Linux and Mac: $HOME/.idapro

See here and here.

NB: Multiple entries are allowed, separated by ; on Windows and : on Linux/Mac.

$IDAUSR

• Cache files (ignored):
  • proccache.lst and proccache64.lst
  • trusted_i64_list.bin and trusted_idb_list.bin
• ida.reg (not on Windows)
• idapythonrc.py will be parsed after IDAPython initialization
• shortcuts.cfg

$IDAUSR/cfg

• ida.cfg
• hexrays.cfgc

$IDAUSR/plugins

Caveats

• The basename is relevant for the plugin (i.e. extension stripped)
• Native extensions take precedence over .idc and .py ones

Other locations inside $IDAUSR

• $IDAUSR/ids/<platform-name>
• $IDAUSR/loaders
• $IDAUSR/procs
• $IDAUSR/sig/<arch>
• $IDAUSR/themes
• $IDAUSR/til/<arch>

Troubleshooting

Command line option -zFC should help to see the files/folders and order in which they get searched.