I believe the feature you are looking for is called 'Unified Folders' which works on both IMAP and POP3 protocols.
The official site location: http://kb.mozillazine.org/Global_Inbox#Unified_Folders
Quote from the site:
Unified Folders (originally named Smart Folders when it was added in
3.0) is a folder pane view which looks like a global inbox account by merging the contents of all inbox folders (both POP, IMAP and local
folders) from all accounts. It also shows the inbox of each account as
a child folder of the unified Inbox account. Any messages in an inbox
shows up in both the root of the unified Inbox, plus the child folder
of the unified Inbox for that account.
To use this functionality:
View >> Folders >> Unified
I have verified that this does work on Thunderbird 12.0.1 using Ubuntu 12.04. The KB article I found above it a bit old but still holds correct information about the functionality of the 'Unified Folders'.
If you are just trying to combine the Inbox only and leave the rest as is, it does not look like it can be done but extensions can be made in the future to have this feature in Thunderbird.
Hope this is helpful.