Revert "put back lyx files"

This reverts commit 40c1b9c022d9a7f0cbef8582af372c749a9cee53.
Revert "merge paper"

This reverts commit e424f13ac31cd66e70f96cc3b39548e97534386a.
Revert "removed lyx files"

This reverts commit 6a074130c2bbf45f55af0fc8f0d424abc6c9a780.
Revert "add ignore"

This reverts commit 19b2aeedd26914759653a636ada536bf2e732f9c.
Revert "update from paper"

This reverts commit 4e4b9095104fc38e0d3a7479247f1b2da1dfa2ce.