[RN] Files in .vscode and .che folders of a git repository are ignored at workspace creation

Synced from Eclipse Che issue

https://github.com/eclipse/che/issues/21635

Describe the bug

All defined plugins from the extensions.json are not installed If create a workspace by the factory and che-theia editor.
Also I see that the tools component doesn't contain environment variables that should be injected by the Dashboard:

        - name: PLUGIN_REMOTE_ENDPOINT_EXECUTABLE
          value: /remote-endpoint/plugin-remote-endpoint
        - name: THEIA_PLUGINS
          value: 'local-dir:///plugins/sidecars/tools'

It's also not possible to customize an editor by using .che/che-editor.yaml file:

Che version

next (development version)

Steps to reproduce

1. Create a workspace by this factory: https://github.com/che-samples/java-spring-petclinic/tree/devfilev2?che-editor=eclipse/che-theia/next
2. Open tools container and check that /plugins folder doesn't exist
3. Go to the Dasboard and check env variables in the tools component

Expected behavior

/plugins folder should be existed and plugins from the .vscode/extensions.json should be installed

Runtime

OpenShift

Screenshots

Installation method

chectl/next

Environment

Linux

Release Notes Text

Files in .vscode and .che subfolders need to be processed during workspace creation as they can contain important workspace details (as the editor and the che-theia plugins to pre-install) but were ignored in recent versions due to a regression. This has been fixed in this release.