Conform to expectations regarding directories for docs and for test-data

[dalito]

The template inherited a slightly unconventional directory layout from linkml-project-cookiecutter.

In most python and many other projects, certain files are stored at different locations. So the template breaks the expectations. We should fix that.

• Source files for the documentation are currently in src/docs. We should move them to docs/. Note that docs/ is currently git-ignored as it is used as build-directory for the documentation. The documentation build directory is already site which is the default for mkdocs (good!).

• Test data used in unit tests are currently in src/data/examples/ but typically stored under tests/....

[dalito]

Problems of current docs-generation:

• possible name clashes between md-files generated for the model elements and those of additional pages (all is put into one folder)
• untypical way of structuring docs and untypical way of generating them makes it more difficult to understand/learn

Proposed changes:

• Change directory where permanent elements of the documentation are stored to the mkdocs standard: docs/
• Create a separate directory where only the generated docs are placed: docs/elements - This is matching the way how auto-generated API-documentation is typically integrated.
• Move: src/docs/template -> docs/templates-linkml (and exclude it in mkdocs.yaml)

I was wondering about a good name for directory of the generated schema-documentation. Candidates: "auto", "elements", "gen", "generated", "schema", ... - My current favorite is "elements" since all schema-elements get a page, and it is also a meaningful word in the URL.

[dalito]

Proposed changes for test data:

• Move folder from src/data/examples to tests/data
• Sub-structure tests/data: Add valid, invalid, problem/valid and problem/invalid folders (as in nmdc schema repo)