Yes, Eagle supports completely self-contained deployment scenarios, including any application scripts you may need. You can end up with a single EXE, if needed.

Also, Eagle runs quite well on Mono, on both Mac OS X and Linux.

I'm not sure what you mean by "Can you run Fossil on this" since Fossil itself is written in C. However, Eagle can certainly be used with Fossil via its Tcl integration support. The Garuda package (part of Eagle) is used to load the CLR and Eagle from native Tcl.

Eagle "knows" about all the .NET primitive types, including generics, nullable value types, ByRef, multi-dimensional and nested arrays, and all delegate types. The "core marshaller" handles all translations between these types and strings. Everything is handled with full fidelity.