Fix handling of tool section during pyproject.toml generation

[dataflake]

Our templates for pyproject.toml contain several tool.coverage sections. Unfortunately, merging those defaults into the contents of the package's own pyproject.toml will simply replace everything under the tool key with the tool contents from our template.

This change captures the tool sections from the package's own pyproject.toml and re-adds all keys under tool with the exception of coverage, which is taken from our template.

Use case where I saw the issue: When moving namespace package discovery settings from setup.py to pyproject.toml a key [tool.setuptools.packages.find] is needed, which was simply gone after running config-package.