Repository: haddocking/haddock3
Issue: Duplicated error messages

Most of the errors/warning are now duplicated;

```
[2022-07-29 09:28:54,264 cli INFO] 
##############################################
#                                            #
#                 HADDOCK 3                  #
#                                            #
##############################################

Starting HADDOCK 3.0.0 on 2022-07-29 09:28:00

Python 3.9.0 | packaged by conda-forge | (default, Nov 26 2020, 07:54:06) 
[Clang 11.0.0 ]

[2022-07-29 09:28:54,305 libutil ERROR] Parameter 'optint' is not a valid general parameter, did you mean 'mdscoring'?
Traceback (most recent call last):
  File "/Users/rodrigo/repos/haddock3/src/haddock/libs/libutil.py", line 305, in log_error_and_exit
    yield
  File "/Users/rodrigo/repos/haddock3/src/haddock/clis/cli.py", line 135, in main
    params, other_params = setup_run(
  File "/Users/rodrigo/repos/haddock3/src/haddock/gear/prepare_run.py", line 185, in setup_run
    validate_module_names_are_not_misspelled(params)
  File "/Users/rodrigo/repos/haddock3/src/haddock/gear/prepare_run.py", line 616, in validate_module_names_are_not_misspelled
    validate_parameters_are_not_misspelled(
  File "/Users/rodrigo/repos/haddock3/src/haddock/gear/prepare_run.py", line 633, in validate_parameters_are_not_misspelled
    raise ValueError(emsg)
ValueError: Parameter 'optint' is not a valid general parameter, did you mean 'mdscoring'?
[2022-07-29 09:28:54,305 libutil ERROR] Parameter 'optint' is not a valid general parameter, did you mean 'mdscoring'?
Traceback (most recent call last):
  File "/Users/rodrigo/repos/haddock3/src/haddock/libs/libutil.py", line 305, in log_error_and_exit
    yield
  File "/Users/rodrigo/repos/haddock3/src/haddock/clis/cli.py", line 135, in main
    params, other_params = setup_run(
  File "/Users/rodrigo/repos/haddock3/src/haddock/gear/prepare_run.py", line 185, in setup_run
    validate_module_names_are_not_misspelled(params)
  File "/Users/rodrigo/repos/haddock3/src/haddock/gear/prepare_run.py", line 616, in validate_module_names_are_not_misspelled
    validate_parameters_are_not_misspelled(
  File "/Users/rodrigo/repos/haddock3/src/haddock/gear/prepare_run.py", line 633, in validate_parameters_are_not_misspelled
    raise ValueError(emsg)
ValueError: Parameter 'optint' is not a valid general parameter, did you mean 'mdscoring'?
[2022-07-29 09:28:54,309 libutil ERROR] Parameter 'optint' is not a valid general parameter, did you mean 'mdscoring'?
[2022-07-29 09:28:54,309 libutil ERROR] Parameter 'optint' is not a valid general parameter, did you mean 'mdscoring'?
[2022-07-29 09:28:54,310 libutil ERROR] An error has occurred, see log file. And contact the developers if needed.
[2022-07-29 09:28:54,310 libutil ERROR] An error has occurred, see log file. And contact the developers if needed.
[2022-07-29 09:28:54,314 libutil INFO] Finished at 29/07/2022 09:28:54. For any help contact us at https://github.com/haddocking/haddock3/issues. Au revoir! Agur! Ciao!.
```



Changed files:
src/haddock/core/defaults.py, src/haddock/__init__.py

diff --git a/src/haddock/__init__.py b/src/haddock/__init__.py
index e8d156d1..43cafa03 100644
--- a/src/haddock/__init__.py
+++ b/src/haddock/__init__.py
@@ -1,15 +1,15 @@
 """HADDOCK3 library."""
 import logging
+import sys
 from pathlib import Path
 
-from haddock.libs.liblog import add_syserr_handler, add_sysout_handler
-
 
 log = logging.getLogger(__name__)
 log.handlers.clear()
 log.setLevel(logging.DEBUG)
-add_sysout_handler(log)
-add_syserr_handler(log)
+handler = logging.StreamHandler(sys.stdout)
+handler.setFormatter(logging.Formatter("[%(asctime)s %(module)s %(levelname)s] %(message)s"))
+log.addHandler(handler)
 
 haddock3_source_path = Path(__file__).resolve().parent
 haddock3_repository_path = haddock3_source_path.parents[1]
diff --git a/src/haddock/core/defaults.py b/src/haddock/core/defaults.py
index 998f77ca..120f8689 100644
--- a/src/haddock/core/defaults.py
+++ b/src/haddock/core/defaults.py
@@ -13,7 +13,7 @@ cns_exec = Path(haddock3_repository_path, "bin", "cns")
 if not cns_exec.exists():
     log.error(
         'CNS executable `bin/cns` not found. '
-        'Did you installed HADDOCK3 properly?'
+        'Please check the install instructions.'
         )
     sys.exit()