feat!: allow specifying the dependency depth resolution through CLI and make dependency resolution off by default

[tromai]

Closes #838 .

In this Pull Request I made the following changes:

• 63b981d I refactor the dependency resolver base class so that it accepts whether it should analyze all transitive dependencies through a method parameter instead of the defaults.ini configuration.

[dependency.resolver] 
   recursive = True

• 076318a I modified the Macaron's CLI to make --skip-deps an no-op. I also added --deps-depth as a new flag for setting the dependency resolution behavior (it's disabled by default).
• a9dbacb, 41e6399, a85e855 I modified the existing test cases given the changes in Macaron's analyze command CLI.
• d30215b I added new integration test cases on invalid usage of --deps-depth:
  • Providing invalid values to --deps-depth
  • Not setting --deps-depth when providing SBOM or Python Virtual Environment as input.
• f2dde1f Update the Sphinx documentation accordingly.

[behnazh-w]

The --skip-deps option is still mentioned in the usage documentation and various tutorials. Could you please remove these references and ensure that the remaining text remains clear and coherent?

[tromai]

The --skip-deps option is still mentioned in the usage documentation and various tutorials. Could you please remove these references and ensure that the remaining text remains clear and coherent?

I have removed the remaining --skip-deps in this commit 8b6ceac.
The only places where --skip-deps exists are within __main__.py and command_analyze.rst. In all cases, there are DEPRECATED messages.