The same thing happens to me too, and the most voted answer 
here 
http://stackoverflow.com/questions/5904256/git-subtree-merge-into-a-deeply-nested-subdirectory
 
helps me.

Clarifying for future readers, the solution is in the comments of Chris 
Johnsen's response. If you're seeing the "fatal: entry not found in tree" 
error, get rid of the trailing slash at the end of your subtree prefix.


在 2013年8月29日星期四UTC+8上午2时26分27秒,Jon Mullen写道:
>
> I have a repository named bar.  I added a sub repository using the 
> following subtree command.
>
> git subtree add --squash -P foodir/ foo master
>
> I then pushed these changes to bar.  A few days ago I made changes to the 
> foo repository and I am now trying to pull them into the bar repository 
> using the following command.
>
> git subtree pull --squash -P foodir/ foo master
>
> However, at the end I receive an error that says the following.
>
> Fatal: entry not found in tree (Some SHA number)
>
> Does anyone have a clue to what I am doing wrong?
>

在 2013年8月29日星期四UTC+8上午2时26分27秒,Jon Mullen写道:
>
> I have a repository named bar.  I added a sub repository using the 
> following subtree command.
>
> git subtree add --squash -P foodir/ foo master
>
> I then pushed these changes to bar.  A few days ago I made changes to the 
> foo repository and I am now trying to pull them into the bar repository 
> using the following command.
>
> git subtree pull --squash -P foodir/ foo master
>
> However, at the end I receive an error that says the following.
>
> Fatal: entry not found in tree (Some SHA number)
>
> Does anyone have a clue to what I am doing wrong?
>

在 2013年8月29日星期四UTC+8上午2时26分27秒,Jon Mullen写道:
>
> I have a repository named bar.  I added a sub repository using the 
> following subtree command.
>
> git subtree add --squash -P foodir/ foo master
>
> I then pushed these changes to bar.  A few days ago I made changes to the 
> foo repository and I am now trying to pull them into the bar repository 
> using the following command.
>
> git subtree pull --squash -P foodir/ foo master
>
> However, at the end I receive an error that says the following.
>
> Fatal: entry not found in tree (Some SHA number)
>
> Does anyone have a clue to what I am doing wrong?
>

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