remove all final mentions of bionemo framework2 (NVIDIA-BioNeMo#1652)

### Description
This commit does a replacement of all mentions of BioNeMo Framework to
BioNeMo Recipes. It also removes old documentation referencing NeMo2 and
previous dependencies of Framework.

### Type of changes

<!-- Mark the relevant option with an [x] -->

- [ ] Bug fix (non-breaking change which fixes an issue)
- [ ] New feature (non-breaking change which adds functionality)
- [ ] Refactor
- [X ] Documentation update
- [ ] Other (please describe):

### CI Pipeline Configuration

Configure CI behavior by applying the relevant labels. By default, only
basic unit tests are run.

-
[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, 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.

For more details, see [CONTRIBUTING](CONTRIBUTING.md)

> [!NOTE]
> By default, only basic unit tests are run. Add appropriate labels to
enable an additional test coverage.

#### Authorizing CI Runs

We use
[copy-pr-bot](https://docs.gha-runners.nvidia.com/apps/copy-pr-bot/#automation)
to manage authorization of CI
runs on NVIDIA's compute resources.

- If a pull request is opened by a trusted user and contains only
trusted changes, the pull request's code will
automatically be copied to a pull-request/ prefixed branch in the source
repository (e.g. pull-request/123)
- If a pull request is opened by an untrusted user or contains untrusted
changes, an NVIDIA org member must leave an
`/ok to test` comment on the pull request to trigger CI. This will need
to be done for each new commit.

#### Triggering Code Rabbit AI Review

To trigger a code review from code rabbit, comment on a pull request
with one of these commands:

- @coderabbitai review - Triggers a standard review
- @coderabbitai full review - Triggers a comprehensive review

See https://docs.coderabbit.ai/reference/review-commands for a full list
of commands.

### Pre-submit Checklist

<!--- Ensure all items are completed before submitting -->

- [ ] I have tested these changes locally
- [ ] I have updated the documentation accordingly
- [ ] I have added/updated tests as needed
- [ ] All existing tests pass successfully

---------

Signed-off-by: Zoey Zhang <zozhang@nvidia.com>

Author: zoeyz101

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -13,7 +13,7 @@ body:
   - type: input
     id: version
     attributes:
-      label: BioNeMo Framework Version
+      label: BioNeMo Recipes Version
       description: |
         **What version or commit hash of the framework are you using?**
 
@@ -89,8 +89,8 @@ body:
     id: docker-image-info
     attributes:
       label: Docker Image
-      description: If the issue occurred in a container, provide the docker image name. Visit [BioNeMo Framework NGC website](https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/containers/bionemo-framework/tags) for available images.
-      placeholder: e.g., nvcr.io/nvidia/clara/bionemo-framework:2.2
+      description: If the issue occurred in a container, provide the docker image name. Visit the [PyTorch NGC Container Registry](https://catalog.ngc.nvidia.com/orgs/nvidia/containers/pytorch) for available images.
+      placeholder: e.g., nvcr.io/nvidia/pytorch:26.05-py3
     validations:
       required: false
 

.github/ISSUE_TEMPLATE/feature-request.yml

@@ -17,7 +17,7 @@ body:
  - type: input
    id: version
    attributes:
-     label: BioNeMo Framework Version
+     label: BioNeMo Recipes Version
      description: What version or commit hash of the framework are you using? Please, specify a commit hash or version tag. Do not use 'latest', 'ToT' or 'nightly' as a reference.
 
      placeholder: commit-hash or version tag, ie v1.2.3.

.github/nv-slack-bot.yaml

@@ -1,20 +1,20 @@
 $schema: https://public.gha-runners.nvidia.com/nv-slack-bot/schemas/config-v1.json
 enabled: true
 notifications:
-  # Send a slack notification when BioNeMo Framework nightly CI fails
-  - name: "BioNeMo Framework Nightly CI Failed"
+  # Send a slack notification when BioNeMo Recipes nightly CI fails
+  - name: "BioNeMo Recipes Nightly CI Failed"
     event: workflow_run
     slack:
       nvidia:
         channels:
           - id: C0832RNTR09 # bionemo-fw-ci-alerts
     match: >
       workflow_run.conclusion = "failure"
-      and workflow_run.name = "BioNeMo Framework CI"
+      and workflow_run.name = "BioNeMo Recipes CI"
       and workflow_run.event = "schedule"
     message:
       body: |
-        <{{url}}|BioNeMo Framework nightly CI "{{name}}"> failed
+        <{{url}}|BioNeMo Recipes nightly CI "{{name}}"> failed
       vars:
         url: workflow_run.html_url
         name: workflow_run.name

docs/docs/SUMMARY.md

@@ -1,3 +1,3 @@
 - [Home](index.md)
-- [BioNeMo Framework](main/)
+- [BioNeMo Recipes](main/)
 - [Models](models/)

docs/docs/main/references/FAQ.md docs/docs/main/FAQ.mddocs/docs/main/references/FAQ.md renamed to docs/docs/main/FAQ.md

@@ -11,16 +11,12 @@ while also providing a high degree of freedom and flexibility for users.
 ## How do I install BioNeMo Recipes?
 
 You can install individual recipe directories from within BioNeMo Recipes by following the corresponding
-README pages the [BioNeMo Recipes GitHub](https://github.com/NVIDIA-BioNeMo/bionemo-framework). Please note that this is a
-beta feature and may require some additional effort to install seamlessly. We are actively working on testing this
-functionality and expect it will be a fully supported feature in future releases. You can review our
-[release notes](../about/releasenotes-fw.md) to stay up to
-date on our releases.
+README pages the [BioNeMo Recipes GitHub](https://github.com/NVIDIA-BioNeMo/bionemo-framework).
 
 ## What are the system requirements for BioNeMo Recipes?
 
 Generally, BioNeMo Recipes should run on any NVIDIA GPU with Compute Capability ≥8.0. For a full list of supported
-hardware, refer to the [Hardware and Software Prerequisites](../getting-started/pre-reqs.md).
+hardware, refer to the [Hardware and Software Prerequisites](getting-started/pre-reqs.md).
 
 ## Can I contribute code or models to BioNeMo Recipes?
 
@@ -33,8 +29,8 @@ tokenizers, custom architecture blocks, and other reusable features over end-to-
 consider end-to-end model implementations on a case-by-case basis. If you're interested in this contribution of this
 kind, we recommend [reaching out to us](https://www.nvidia.com/en-us/industries/healthcare/contact-sales/) first
 
-For more information about external contributions, refer to the [Contributing](../contributing/contributing.md) and
-[Code Review](../contributing/code-review.md) pages.
+For more information about external contributions, refer to the [Contributing](contributing/contributing.md) and
+[Code Review](contributing/code-review.md) pages.
 
 ## How do I report bugs or suggest new features?
 

docs/docs/main/SUMMARY.md

@@ -4,4 +4,4 @@
 - [Tutorials](examples/)
 - [Data Sets](datasets/)
 - [Contributing](contributing/)
-- [References](references/)
+- [Frequently Asked Questions](FAQ.md)

docs/docs/main/about/SUMMARY.md

@@ -1,3 +1 @@
 - [Overview](overview.md)
-- [Background](background/)
-- [Release Notes](releasenotes-fw.md)