Custom Modifications:

*.css
Modified occurrences of url() from using a plain path to a JSF resource expression path.

/ckeditor.mapping.js
Added this file to specify a mapping from canonical resource names to correct JSF resource URLs.
Modified mappings of *.md files to *.md.txt, so they have a known mime type

/ckeditor.js
/plugins/smiley/dialogs/smiley.js
/plugins/wsc/dialogs/wsc.js
/plugins/wsc/dialogs/wsc_ie.js
/plugins/about/dialogs/about.js
Modified paths to internal resources to invoke CKEDITOR.getUrl() first, in order to use correct JSF URLs.

/ckeditor.js
Line 778, added object existence conditions in detach() function to avoid NPEs
Line 904, set specific height when entering into source mode, in order to avoid collapsing the editable area

/samples
Removed all resources under /samples and the directory itself.

*.md
Renamed *.md files to *.md.txt, so they have a known mime type

/plugins/wsc/dialogs/wsc.js
/plugins/wsc/dialogs/wsc_ie.js
Replaced occurrences of the "http:" string for document.location.protocol, in order to correctly support SSL