I just tried upgrading my LCDS 2.5 installation to LCDS 2.6. One difference I noticed is that the lcds.war file no longer contains a number of files in the previous release, such as flex-bootstrap.jar. This causes error messages complaining of a missing flex.bootstrap.BootstrapServlet class, among other things.
1. Where did this file go?
2. Is there a migration guide for upgrading to LCDS 2.6? I'm sure flex-bootstrap.jar is just the tip of the iceberg. There are other issues too like automation.swc no longer being in flex-sdk.
WebTier compiler is not longer shipped with LCDS 2.6 - that's why this jar is not included. You should remove the reference to BootstrapServlet from web.xml.