"In" can also mean no longer than a particular period of time:

1. Can you finish the job in two weeks?

2. Can you finish the job within two weeks?
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The definition is from a dictionary. In this case are both the same?

3. We finished the whole project in a week.

4. We finished the whole project within a week.
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Does #3 mean the following?
3-1. It took a week for us to finish the project.
Or does #3 mean #4?

1 and 2 mean the same thing.

3 and 3-1 are pretty close in meaning.
4 is very close; it means it took no longer than a week to finish the project.

Yes, in both cases, "in" and "within" can be used interchangeably to mean no longer than a particular period of time. For example:

1. Can you finish the job in two weeks? (Can you complete the job in a maximum of two weeks?)
2. Can you finish the job within two weeks? (Can you complete the job, ensuring it is done before or at the end of two weeks?)

Similarly:
3. We finished the whole project in a week. (It took a week for us to finish the project.)
4. We finished the whole project within a week. (We completed the project before or at the end of a week.)

So, in the case of #3, it means that it took a week for the project to be completed. It does not mean the same thing as #4.