The documentation for NetFx:NativeImage states that setting the 
AppBaseDirectory property is optional on executables:

For EXE assemblies, this attribute does not need to be set because NGen will 
use the directory of the assembly file by default.

However, we've found this is not the case and if we don't specify it the 
command line passed to NGen is incorrect and NGening fails.

Is this a known issue?

Neil
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