Here is why MySQL cannot see those files: The system tablespace (ibdata1) has a Storage-Engine specific data dictionary that lets InnoDB map out potential table usage:
Moving InnoDB tables from one place to another requires commands like
ALTER TABLE tblname DISCARD TABLESPACE;
ALTER TABLE tblname IMPORT TABLESPACE;
Here is a part of the MySQL 5.5 Documentation explaining what needs to be considered
Portability Considerations for .ibd Files
You cannot freely move .ibd files between database directories as you
can with MyISAM table files. The table definition stored in the InnoDB
shared tablespace includes the database name. The transaction IDs and
log sequence numbers stored in the tablespace files also differ
between databases.
To move an .ibd file and the associated table from one database to
another, use a RENAME TABLE statement:
RENAME TABLE db1.tbl_name TO db2.tbl_name; If you have a “clean”
backup of an .ibd file, you can restore it to the MySQL installation
from which it originated as follows:
The table must not have been dropped or truncated since you copied the
.ibd file, because doing so changes the table ID stored inside the
tablespace.
Issue this ALTER TABLE statement to delete the current .ibd file:
ALTER TABLE tbl_name DISCARD TABLESPACE; Copy the backup .ibd file to
the proper database directory.
Issue this ALTER TABLE statement to tell InnoDB to use the new .ibd
file for the table:
ALTER TABLE tbl_name IMPORT TABLESPACE; In this context, a “clean”
.ibd file backup is one for which the following requirements are
satisfied:
There are no uncommitted modifications by transactions in the .ibd
file.
There are no unmerged insert buffer entries in the .ibd file.
Purge has removed all delete-marked index records from the .ibd file.
mysqld has flushed all modified pages of the .ibd file from the buffer
pool to the file.
Given these caveats and protocols, here is a suggested course of action
For this example, let's try to restore the tags table to the mydb database
STEP #1
Make sure you have backups of those .frm and .ibd files in /tmp/innodb_data
STEP #2
Get the CREATE TABLE tags statement and execute it as CREATE TABLE mydb.tags .... Make sure it is the exact same structure as the original tags.frm
STEP #3
Delete the empty tags.ibd using MySQL
ALTER TABLE mydb.tags DISCARD TABLESPACE;
STEP #4
Bring in the backup copy of tags.ibd
cd /var/lib/mysql/mydb
cp /tmp/innodb_data.tags.ibd .
chown mysql:mysql tags.ibd
STEP #5
Add tags table to the InnoDB Data Dictionary
ALTER TABLE mydb.tags IMPORT TABLESPACE;
STEP 6
Test the table's accessibility
SHOW CREATE TABLE mydb.tags\G
SELECT * FROM mydb.tags LIMIT 10;
If you get normal results, congratulations you import an InnoDB table.
STEP 7
In the future, please don't delete ibdata1 and its logs
Give it a Try !!!
I have discussed things like this before
CAVEAT
What if you do not know the table structure of the tags ?
There are tools to get the CREATE TABLE statement just using the .frm file. I wrote a post about this as well : How can extract the table schema from just the .frm file?. In that post, I copied a .frm file to a Windows machine from a Linux box, ran the Windows tool and got the CREATE TABLE statement.
