Update the e2e flow tutorial to fix errors of generate

[iseeyuan]

Context

What is the purpose of this PR? Is it to

• add a new feature
• fix a bug
• update tests and/or documentation
• other (please add here)

Please link to any issues this PR addresses.

Changelog

What are the changes made in this PR?
When running the tutorial as is, there's error message:

ValueError: The output directory cannot be the same as or a subdirectory of the checkpoint directory. Found ckpt_dir=PosixPath('/tmp/torchtune/llama3_2_3B/lora_single_device/epoch_0') and out_dir=PosixPath('/tmp/torchtune/llama3_2_3B/lora_single_device/epoch_0')

• The fix is to add a specific checkpoint_dir and make it different from the output_dir.

Then I saw the second error:

...
  File "/home/myuan/src/torchtune/recipes/generate.py", line 113, in convert_prompt_to_tokens
    Message(role="user", content=prompt["user"]),
TypeError: string indices must be integers

• The fix is to remove the prompt option from run. It's redundant with the prompt in the .yaml file anyway.

Test plan

Please make sure to do each of the following if applicable to your PR. If you're unsure about any one of these just ask and we will happily help. We also have a contributing page for some guidance on contributing.

• run pre-commit hooks and linters (make sure you've first installed via pre-commit install)
• add unit tests for any new functionality
• update docstrings for any new or updated methods or classes
• run unit tests via pytest tests
• run recipe tests via pytest tests -m integration_test
• manually run any new or modified recipes with sufficient proof of correctness
• include relevant commands and any other artifacts in this summary (pastes of loss curves, eval results, etc.)

UX

If your function changed a public API, please add a dummy example of what the user experience will look like when calling it.
Here is a docstring example
and a tutorial example

• I did not change any public API
• I have added an example to docs or docstrings

[pytorch-bot]

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[RdoubleA]

Looks great! just one small comment

[RdoubleA]

could you try running this?
tune run generate --config ./custom_generation_config.yaml prompt.user="Tell me a joke. "

if that works fine, would prefer including this as an example just to be explicit

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 23.95%. Comparing base (f47f633) to head (5d1280e).
Report is 20 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2251      +/-   ##
==========================================
- Coverage   24.00%   23.95%   -0.06%     
==========================================
  Files         357      358       +1     
  Lines       21094    21205     +111     
==========================================
+ Hits         5064     5080      +16     
- Misses      16030    16125      +95     

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