I had the same error.
The reason is that the link of prototype.js in /usr/share/typo3-src/...
is pointing to /usr/share/javascript/prototype/prototype-1.6.0.js. In
Debian testing (squeeze) with all actual updates this file isn't available.
On my system prototype was installed with version 1.6.1. So the link
could point to /usr/share/javascript/prototype/prototype-1.6.1.js.
But there are some links in /usr/share/javascript/prototype/ who are
pointing to prototype-1.6.1.js. So the link of prototype.js in
/usr/share/typo3-src/... could point the link
/usr/share/javascript/prototype/prototype.js. With this setting you
don't worry about which version of prototype is installed. Only the
maintainer of the package libjs-prototype has to ensure that the link
from /usr/share/javascript/prototype/prototype.js to
/usr/share/javascript/prototype-<version>.js exists.
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