You should be able to start the purge using the command line, by reproducing the same link as the "Purge now" link.

(In [6482]) Refs #3199

Do you mean calling the script via wget? That way, the script would still be influenced by the PHP limitations. I thought more of a shell script solution.

No I mean running it on the command line eg.

/usr/bin/php piwik/index.php -- "module=X&action=Y&etc."

I haven't tried but if you replace the module=X... by the URL it should run in CLI ?

The URL from "purge DB now" looks like this:
index.php?module=PrivacyManager&action=privacySettings&idSite=2&period=day&date=yesterday#

The only difference to the URL already opened is the "#" at the end, so I guess this will call some AJAX stuff which I cannot start from the CLI. Please correct me if I am wrong.

In case this works, would it show information about what is being done? That is the main problem why Im asking, as the purge run over night took ~10 hours to complete (purging from 5 to 4.2 gb) and I could only have a look at the SQL statements being run by using "MySQL Administrator" but didnt get any feedback/status from Piwik (or I couldnt find it).

Therefore, a user might assume that the process is stalled and kill the process.

UNfortunately it won't show the information being done, for that using the mysql admin tool is the best.