Clion is modifying existing Makefile when loading a new project,

I am trying to load a complex Makefile project into CLion and I find that Clion is failing to index the project correctly. On closer inspection I find that CLion is modifying the exisiting Makefile so that crucial subdirectories are not being indexed. And that ruins it for us. Any thoughts? Any way to stop this?

Here's the diff:

[-bash: ~/OPeNDAP/hyrax/bes] diff Makefile mf.orig

121,122c121,122

< #am__append_4 = dap dapreader

< #am__append_5 = modules

---

> am__append_4 = dap dapreader

> am__append_5 = modules

325,330c325,330

< DAP_CFLAGS = 

< DAP_CLIENT_CFLAGS = 

< DAP_CLIENT_LIBS = 

< DAP_CLIENT_STATIC_LIBS = 

< DAP_CONFIG = no

< DAP_LIBS = 

---

> DAP_CFLAGS = -I/Users/ndp/OPeNDAP/hyrax/build/include -I/Users/ndp/OPeNDAP/hyrax/build/include/libdap -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include 

> DAP_CLIENT_CFLAGS = -I/Users/ndp/OPeNDAP/hyrax/build/include -I/Users/ndp/OPeNDAP/hyrax/build/include/libdap -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include 

> DAP_CLIENT_LIBS = -L/Users/ndp/OPeNDAP/hyrax/build/lib64 -L/Users/ndp/OPeNDAP/hyrax/build/lib -ldap -ldapclient -lcurl -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -lpthread  

> DAP_CLIENT_STATIC_LIBS = -L/Users/ndp/OPeNDAP/hyrax/build/lib64 -L/Users/ndp/OPeNDAP/hyrax/build/lib -ldap -ldapclient -lcurl -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -lpthread  

> DAP_CONFIG = /Users/ndp/OPeNDAP/hyrax/build/bin/dap-config

> DAP_LIBS = -L/Users/ndp/OPeNDAP/hyrax/build/lib64 -L/Users/ndp/OPeNDAP/hyrax/build/lib -ldap -ldapserver -ldapclient -lcurl -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -lpthread  

332,335c332,335

< DAP_SERVER_CFLAGS = 

< DAP_SERVER_LIBS = 

< DAP_SERVER_STATIC_LIBS = 

< DAP_STATIC_LIBS = 

---

> DAP_SERVER_CFLAGS = -I/Users/ndp/OPeNDAP/hyrax/build/include -I/Users/ndp/OPeNDAP/hyrax/build/include/libdap -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include 

> DAP_SERVER_LIBS = -L/Users/ndp/OPeNDAP/hyrax/build/lib64 -L/Users/ndp/OPeNDAP/hyrax/build/lib -ldap -ldapserver -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -lpthread  

> DAP_SERVER_STATIC_LIBS = -L/Users/ndp/OPeNDAP/hyrax/build/lib64 -L/Users/ndp/OPeNDAP/hyrax/build/lib -ldap -ldapserver -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -lpthread  

> DAP_STATIC_LIBS = -L/Users/ndp/OPeNDAP/hyrax/build/lib64 -L/Users/ndp/OPeNDAP/hyrax/build/lib -ldap -ldapserver -ldapclient -lcurl -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -lpthread