!112: fix: Database now contains an expected all_samples

Corresponds to the bob.bio.base equivalent, allowing the use of pad Database with bio commands (like bob bio annotate).

Be more lenient with the dependencies version pinning.

!105: Resolve "Switch to new CI/CD configuration"

!106: Autoupdate pre-commit and apply on all files

!107: Fix the database name parameter not followed to bob.pipelines

!108: [pyproject.toml] Changing documentation link to master/sphinx

!109: Replace clapp by clapper.

!110: meta [readme]: Switch the README.rst to markdown

Renames README.rst to README.md to be supported by the release script.

!111: meta(deps): add bob as dependency in new structure

Adapt to the new structure of bob with bob/bob on top.