It seems like the "Additional properties" for the manifest file lose their carriage returns on my system after awhile. I went back the next day and they were all in one row.
I had some existing bundles with bnd files. I went into Project Settings, added an Osmorc facet, set the Manifest file policy to Controlled by Osmorc, then pasted the contents of my bnd file into "Additional Properties". I then deleted the symbolic name, activator, and version from the additional properties and copied their values up into the special fields. I clicked ok.
I then created an OSGI run target that included my bundle. At that point I had to go home. When I booted everything up the next day, all the CRs were gone from Additional Properties-- all the text was together on one line.