Tool annotation imports breaking the package structure

[nsoranzo]

Describe the bug
Currently we are not enforcing the package structure described in packages/packages_by_dep_dag.txt when it comes to Python type checking by using if TYPE_CHECKING:.
This allows us to have more precise type annotations but also hides problems that we should fix, so this is a tracking issue for them:

• lib/galaxy/config/__init__.py: from galaxy.model import User
• lib/galaxy/objectstore/__init__.py: from galaxy.model import Dataset, DatasetInstance
• lib/galaxy/schema/fields.py: from galaxy.security.idencoding import IdEncodingHelper
• lib/galaxy/tool_util/data/__init__.py: from galaxy.tools.data_manager.manager import DataManager
• lib/galaxy/tool_util/deps/__init__.py: from galaxy.jobs import JobDestination
• lib/galaxy/tool_util/deps/views.py: from galaxy.structured_app import StructuredApp
• lib/galaxy/tool_util/parser/cwl.py: from galaxy.tools import Tool
• lib/galaxy/tool_util/parser/interface.py: from galaxy.tools import Tool
• lib/galaxy/tool_util/toolbox/base.py: from galaxy.model import DynamicTool
• lib/galaxy/model/__init__.py: from galaxy.tools import DefaultToolState
• lib/galaxy/model/__init__.py: from galaxy.workflow.modules import WorkflowModule
• lib/galaxy/model/store/__init__.py: from galaxy.managers.workflows import WorkflowContentsManager
• lib/galaxy/model/store/discover.py: from galaxy.job_execution.output_collect import DatasetCollector, ToolMetadataDatasetCollector
• lib/galaxy/workflow/run.py: from galaxy.webapps.base.webapp import GalaxyWebTransaction
• lib/galaxy/workflow/run_request.py: from galaxy.webapps.base.webapp import GalaxyWebTransaction