issues with Neovim, in specific with the init.nvim file

I spent some hours customizing neovim but now when I edit the init.nvim file it doesn't recognize the set command and there is no syntax highlighting. Can somebody help me? nvim --version: v0.3.4.

When I run :checkhealth the output is:

health#nvim#check
========================================================================
## Configuration
  - WARNING: Missing user config file: /home/barbieri/.config/nvim/init.vim
    - ADVICE:
      - :help nvim-from-vim

## Performance
  - OK: Build type: Release

## Remote Plugins
  - OK: Up to date

## terminal
  - INFO: key_backspace (kbs) terminfo entry: key_backspace=\177
  - INFO: key_dc (kdch1) terminfo entry: key_dc=\E[3~

health#provider#check
========================================================================
## Clipboard (optional)
  - OK: Clipboard tool found: xclip

## Python 2 provider (optional)
  - INFO: `g:python_host_prog` is not set.  Searching for python2 in the environment.
  - INFO: Executable: /usr/bin/python2
  - INFO: Python version: 2.7.16
  - INFO: pynvim version: 0.3.0 (outdated; from /usr/lib/python2.7/dist-packages/neovim)
  - WARNING: Latest pynvim is NOT installed: 0.4.3

## Python 3 provider (optional)
  - WARNING: No Python executable found that can `import neovim`. Using the first available executable   for diagnostics.
  - ERROR: Python provider error:
    - ADVICE:
      - provider/pythonx: Could not load Python 3:
          /usr/bin/python3 does not have the "neovim" module. :help provider-python
          python3.7 not found in search path or not executable.
          python3.6 not found in search path or not executable.
          python3.5 not found in search path or not executable.
          python3.4 not found in search path or not executable.
          python3.3 not found in search path or not executable.
          /usr/bin/python is Python 2.7 and cannot provide Python 3.
  - INFO: Executable: Not found
## Ruby provider (optional)
  - WARNING: `ruby` and `gem` must be in $PATH.
    - ADVICE:
      - Install Ruby and verify that `ruby` and `gem` commands work.

## Node.js provider (optional)
  - WARNING: `node` and `npm` (or `yarn`) must be in $PATH.
    - ADVICE:
      - Install Node.js and verify that `node` and `npm` (or `yarn`) commands work.

I don't have python2 installed and my python3 version is 3.9.2 (but it works and there is synatx highlighting). I saved my init.nvim file as .config/nvim/init.nvim in the directories .config and then nvim. Is there also a way to reset neovim?