Drop old code to sync files on server filesystem. Clean cli, init paths

This stale code was originally used to index files on server file
system directly by server. We currently push files to sync via API.

Server side syncing of remote content like Github and Notion is still
supported. But old, unused code for server side sync of files on
server fs is being cleaned out.

New --log-file cli args allows specifying where khoj server should
store logs on fs. This replaces the --config-file cli arg that was
only being used as a proxy for deciding where to store the log file.

- TODO
  - Tests are broken. They were relying on the server side content
    syncing for test setup

tests/test_client.py

@@ -283,10 +283,6 @@ def test_get_api_config_types(client, sample_org_data, default_user: KhojUser):
 def test_get_configured_types_with_no_content_config(fastapi_app: FastAPI):
     # Arrange
     state.anonymous_mode = True
-    if state.config and state.config.content_type:
-        state.config.content_type = None
-    state.search_models = configure_search_types()
-
     configure_routes(fastapi_app)
     client = TestClient(fastapi_app)