<sub>*Wiki answer generated from question comments by [akuzminsky][1]*</sub>

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If you see `*.ibd` files then `innodb_file_per_table` is `ON`, otherwise all tables would be in `ibdata1`.

If it tells a table doesn't exists then the table is missing in InnoDB dictionary. Try to dump all tables into separate sql dumps (one table - one file). Those tables you can't dump you can restore with [TwinDB recovery toolkit][2].

There are no binary packages yet. You have to get source code from launchpad and compile it. See instructions at [Recover InnoDB dictionary][3]. It's pretty straightforward:

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    bzr lp:undrop-for-innodb 

and then 

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    make all


  [1]: http://dba.stackexchange.com/users/34361/akuzminsky
  [2]: https://launchpad.net/undrop-for-innodb
  [3]: https://twindb.com/how-to-recover-innodb-dictionary/