migration of bionemo-recipes to top-level directory (NVIDIA-BioNeMo#1633)

Prepares the repo to be renamed "BioNeMo Recipes", dropping our
`sub-packages` structure and lingering CI / references to the legacy
framework container.

The legacy code has been moved to the bionemo2 branch.

Closes BIO-743

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

* **Chores**
* Reorganized repository structure to top-level `models/`, `recipes/`,
and `interpretability/` directories
  * Removed dev container configuration and related tooling
* Removed legacy CI workflows for sub-packages and performance
benchmarking
* Updated CI labels and recipe testing workflow to include notebook test
coverage
* Simplified documentation to focus on BioNeMo Recipes with updated
directory references

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Peter St. John <pstjohn@nvidia.com>

Author: pstjohn

.cursorrules

@@ -1,3 +1,3 @@
-# Dev Container Setup
+# BioNeMo Recipes Dev Container
 
-General-purpose dev container for local recipe development.
+General-purpose dev container for local BioNeMo Recipes development.

.devcontainer/README.md

@@ -1,5 +1,5 @@
 {
-    "name": "BioNeMo Dev Container",
+    "name": "BioNeMo Recipes Dev Container",
     "build": {
         "dockerfile": "Dockerfile"
     },

.devcontainer/devcontainer.json

@@ -24,7 +24,9 @@ updates:
 
   - package-ecosystem: "uv"
     directories:
-      - "/bionemo-recipes/**"
+      - "/models/**"
+      - "/recipes/**"
+      - "/interpretability/**"
     target-branch: "main"
     schedule:
       interval: "weekly"
@@ -37,7 +39,9 @@ updates:
 
   - package-ecosystem: "pip"
     directories:
-      - "/bionemo-recipes/**"
+      - "/models/**"
+      - "/recipes/**"
+      - "/interpretability/**"
     target-branch: "main"
     schedule:
       interval: "weekly"
@@ -50,7 +54,9 @@ updates:
 
   - package-ecosystem: "npm"
     directories:
-      - "/bionemo-recipes/**"
+      - "/models/**"
+      - "/recipes/**"
+      - "/interpretability/**"
     target-branch: "main"
     schedule:
       interval: "weekly"

.github/dependabot.yml

@@ -8,13 +8,9 @@
   color: 1D76DB  # Blue
 
 - name: ciflow:all
-  description: Run all tests (unit tests, slow tests, and notebooks). This label can be used to enforce running all framework tests.
+  description: Run all tests, including unit tests, slow tests, notebooks, and every recipe/model directory.
   color: FBCA04  # Yellow/Gold
 
-- name: ciflow:all-recipes
-  description: Run tests for all recipes (under bionemo-recipes). This label can be used to enforce running tests for all recipes.
-  color: 812afe  # Purple
-
 - name: ciflow:skip
   description: Skip all CI tests for this PR
   color: B60205  # Red

.github/labels.yml

@@ -27,8 +27,7 @@ Configure CI behavior by applying the relevant labels. By default, only basic un
 - [ciflow:skip](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/main/contributing/contributing.md#ciflow:skip) - Skip all CI tests for this PR
 - [ciflow:notebooks](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/main/contributing/contributing.md#ciflow:notebooks) - Run Jupyter notebooks execution tests
 - [ciflow:slow](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/main/contributing/contributing.md#ciflow:slow) - Run slow single GPU integration tests marked as @pytest.mark.slow
-- [ciflow:all](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/main/contributing/contributing.md#ciflow:all) - Run all tests (unit tests, slow tests, and notebooks). This label can be used to enforce running all framework tests.
-- [ciflow:all-recipes](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/main/contributing/contributing.md#ciflow:all-recipes) - Run tests for all recipes (under bionemo-recipes). This label can be used to enforce running tests for all recipes.
+- [ciflow:all](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/main/contributing/contributing.md#ciflow:all) - Run all tests, including unit tests, slow tests, notebooks, and every recipe/model directory.
 
 Unit tests marked as `@pytest.mark.multi_gpu` or `@pytest.mark.distributed` are not run in the PR pipeline.