Up to MySQL 5.1.30, the InnoDB Plugin replaced the
  built-in InnoDB in MySQL when the server was started with the option skip_innodb.
  Due to MySQL Bug#42610, it was impossible to replace the built-in InnoDB in MySQL with a
  plugin in MySQL 5.1.31 and 5.1.32.  MySQL 5.1.33 introduced the
  option ignore_builtin_innodb to allow InnoDB Plugin
  installation in the binary release.
Up to MySQL 5.1.30, installing the binary InnoDB Plugin
  requires that MySQL be shut down and restarted after issuing
  the INSTALL PLUGIN statements.  This is because
  the INSTALL PLUGIN statement started the plugin
  with default options.  The options would only be read from the
  option file (my.cnf or my.ini)
  after restarting the server.  The InnoDB Plugin worked around this
  limitation by copying parameters from the internal data structures
  of the built-in InnoDB in MySQL.  Beginning with MySQL 5.1.33,
  the INSTALL PLUGIN statement re-reads the
  option file and passes all options to the plugin, even those that are
  not recognized by the built-in InnoDB in MySQL.
To use the binary InnoDB Plugin with MySQL 5.1.30 or
  earlier, you may follow the instructions given in
  Section 9.3, “Installing the Precompiled InnoDB Plugin as a Shared Library”, with one
  change: Replace the option ignore_builtin_innodb with
  skip_innodb.  The general steps for dynamically
  installing the binary InnoDB Plugin are thus as follows:
Make sure the MySQL server is not running, using a “slow” shutdown.
Prepend each InnoDB option
    with loose_,
    e.g., loose_innodb_file_per_table instead
    of innodb_file_per_table, so that MySQL
    starts even when InnoDB is unavailable.
Add skip_innodb
    and default_storage_engine=MyISAM to the options,
    to prevent the built-in InnoDB from starting.
Start the MySQL server.
INSTALL the InnoDB Plugin and the
    Information Schema tables, using the supplied script or equivalent
    commands.
Verify the installation of the plugins.
Shut down and reconfigure the MySQL server by editing the appropriate configuration file to use InnoDB as the default engine (if desired), and set appropriate configuration parameters to enable use of new InnoDB Plugin features.
This change only affects the binary distributions of MySQL and InnoDB Plugin. The procedure for building from source code is unchanged.
This is the User’s Guide for InnoDB Plugin 1.0.6 for MySQL 5.1, generated on March 4, 2010 (rev 673:680M).

