Some more LTRdigest fixes, part II

This PR makes sure that pHMM IDs with directory separators ('/') are processed before using them to craft filenames. This has lead to one case where a GyDB ID (`AP_ty1/copia`) caused LTRdigest to try and write into a subdirectory.
The second fix is a more specific pattern for the unwanted CS/RF/PP lines in HMMER alignment output -- this may need a rework later on but this fix should work for now.