Hi Martin,

* How can I start a workflow with data from my computer if the upload step is not available for workflows?

You'll need to upload the data manually before starting the workflow on the data.

* What should I do for my new tools (added in my own Galaxy installation) to be able to participate in workflows. Anything specila to add in their XML description file perhaps? [Perhaps this question is more for the galaxy-dev mailing list?]

Once you've verified that your tool is running in Galaxy, you'll be able to use it in a workflow without further modification. Nothing special needs to be done in the XML.

* Is there perhaps more documentation on Galaxy workflows anywhere?

There are screencasts that describe workflows (#s 4 and 5) from a user perspective: http://main.g2.bx.psu.edu/u/aun1/p/screencasts

In general, the Galaxy wiki has much useful information for tool developers: http://bitbucket.org/galaxy/galaxy-central/wiki/SiteMap

Best,
J.