Installation on Apache 2.4

I’m unable to install Piwik on Apache 2.4.
The automatic installation is not working on Apache 2.4, because the generated .htaccess file is invalid. It generates the error :

F:/wwwpiwik/plugins/.htaccess: Invalid command 'Deny', perhaps misspelled or defined by a module not included in the server configuration

It is not possible to get it work by editing these files manually, because the installation script rewrites them when refreshing the installation page.

How can I get the installation process working ?

I found a ticket relating to this issue, that is marked as closed (generated .htaccess files should be wrapped by ifmodule · Issue #3129 · matomo-org/matomo · GitHub), but the problem still exists even with the latest build of piwik (as of today 8 May 2014)

I solved the problem with the following workaround:
[li] I edited each .htaccess file manually
[/li][li] I set each .htaccess file read only

Can you please list what changes you had to make to the htaccess files? Ideally comment on that ticket generated .htaccess files should be wrapped by ifmodule · Issue #3129 · matomo-org/matomo · GitHub

or here if you prefer. There may be something we missed (but it works for me on apache 2.4 but there are so many diferent types of configurations possible)