JakubMisek hi, it looks like LSP is throwing an exception: (I tried reproducing the error on a smaller project but it didn't give the error). Perhaps the inotify issue is one of the reasons why large projects are indexed with missing files.
sudo sysctl fs.inotify.max_user_instances=1024 saved me temporarily
[Info - 11:00:46 PM] Deleting /home/gingdev/.local/share/DEVSENSE/packages-cache ...
[Info - 11:00:46 PM] Deleting DEVSENSE/packages-cache ...
[Info - 11:00:48 PM] Processing packages in /home/gingdev/Code/php/slog/vendor/composer/installed.json ...
[Error - 11:01:03 PM] AggregateException_ctor_DefaultMessage (IOException_INotifyInstanceUserLimitExceeded_Value, 128)
[Error - 11:01:03 PM] AggregateException_ctor_DefaultMessage (IOException_INotifyInstanceUserLimitExceeded_Value, 128)
[Error - 11:01:03 PM] AggregateException_ctor_DefaultMessage (IOException_INotifyInstanceUserLimitExceeded_Value, 128)
[Error - 11:01:03 PM] AggregateException_ctor_DefaultMessage (IOException_INotifyInstanceUserLimitExceeded_Value, 128)
[Error - 11:01:03 PM] AggregateException_ctor_DefaultMessage (IOException_INotifyInstanceUserLimitExceeded_Value, 128)
[Error - 11:01:03 PM] AggregateException_ctor_DefaultMessage (IOException_INotifyInstanceUserLimitExceeded_Value, 128)
[Error - 11:01:03 PM] AggregateException_ctor_DefaultMessage (IOException_INotifyInstanceUserLimitExceeded_Value, 128)
[Error - 11:01:03 PM] AggregateException_ctor_DefaultMessage (IOException_INotifyInstanceUserLimitExceeded_Value, 128)
[Error - 11:01:04 PM] AggregateException_ctor_DefaultMessage (IOException_INotifyInstanceUserLimitExceeded_Value, 128)
[Error - 11:01:04 PM] AggregateException_ctor_DefaultMessage (IOException_INotifyInstanceUserLimitExceeded_Value, 128)
[Info - 11:01:04 PM] Processing done in 00:00:15.4013457.
[Info - 11:01:34 PM] Storing package api-platform/core@v3.1.16 cache ...
[Info - 11:01:34 PM] Storing package behat/transliterator@v1.5.0 cache ...
[Info - 11:01:34 PM] Storing package dflydev/dot-access-data@v3.0.2 cache ...
...