Since Indy is now built-into the install process of Delphi 2009... is there a proper way to 'remove' it so it can be upgraded to the latest from the SVN repo? There isn't an automated option to remove it as far as I'm aware.
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3The dcu files for Indy are stored separately from the other Delphi units. To stop using them, simply remove that directory from the search path, library path, etc., and remove the source files from the browse path.
You can remove the design-time packages the same as any other design-time packages. Remove them from the IDE configuration, and then delete the bpl and dcp files. (If you just delete the files, you may get errors when you next start the IDE since it won't find the expected files.)
Once the Indy components no longer appear on the Tool Palette, the packages no longer appear on the package list, and compiling a project that references Indy units fails with a "can't find used unit" error, you're ready to start installing the latest version.
As Rob already said: Just remove the direcories from Delphi's configuration. An additional step is required though: After each update, make sure they have not been added again! Some of the Delphi 2007 updates apparently did that and I missed it for quite a while until I stumbled upon a bug that I already thought fixed.
I didn't use Delphi 2009, but in older versions of Delphi the installation of Indy components was optional. So you could try launching the setup for Delphi 2009 and see if there is an option to "Add/Remove features" or something similar and use it to remove Indy.
Also, you can customize which packages should be loaded in a project, so you can simply deselect the Indy 10 one and add the one from SVN on a per-project basis (you can also configure the default configuration for projects).
PS. Indy rocks! :-)