clarify remaining improperly scoped (and deprecated) inits

pyproject.toml

@@ -30,9 +30,15 @@ select = ["F401"] # TODO: eventually, expand to other 'I', 'D', and other 'F' li
 fixable = ["ALL"]
 
 [tool.ruff.lint.per-file-ignores]
-"__init__.py" = ["I"]  # Must maintain explicit order for imports for check registration
-"nwbinspector/__init__.py" = ["F401", "I"]  # Temporarily keeping all exposure for back-compatibility
-"inspector_tools/__init__.py" = ["F401", "I"] # Temporarily keeping all exposure for back-compatibility
+"src/nwbinspector/__init__.py" = ["I"]  # Must maintain explicit order for imports for check registration
+"src/nwbinspector/utils/__init__.py" = ["F401", "I"]  # Several items planned for long-term deprecation
+
+# Temporarily keeping all exposure below for back-compatibility
+# Deprecation scheduled for 9/15/2024
+"src/nwbinspector/nwbinspector/__init__.py" = ["F401", "I"]
+"src/nwbinspector/inspector_tools/__init__.py" = ["F401", "I"]
+"src/nwbinspector/version/__init__.py" = ["F401", "I"]
+"src/nwbinspector/register_checks/__init__.py" = ["F401", "I"]
 
 
 [tool.codespell]