submodule upate --remote on these submodules
Using Carton (and Pallet) now to manage dependencies through MELPA and ELPA.

List of old packages to match before: ace-jump-mode, browse-kill-ring, carton, dired-details, expand-region, feature-mode, frame-cmds, frame-fns, groovy-mode, helm, helm-git, magit, markdown-mode, multiple-cursors, org, org-bullets, smart-forward, smex, stripe-buffer, zoom-frm

List of New packages I haven't had before:
ace-jump-buffer, dired+, dired-details+, helm-gist, ibuffer-vc, markdown-mode+, melpa, pallet

Packages that aren't exactly working right now:
gist

Packages That I don't know where it came from (dependencies most likely):
deferred, fit-frame
Changing the jacobo/ config files per mode, no more require and such.  also, seeing as this whole port is not complete jacobo.el has many changes that need to be uncommented / deleted when they are fixed.  Changed jacobo file are:

jacobo/browse-kill-ring.el, jacobo/dired-setup.el, jacobo/expand-region.el, jacobo/feature-mode.el, jacobo/groovy.el, jacobo/helm-mode.el, jacobo/markdown-mode.el, jacobo/multiple-cursors.el, jacobo/org-mode.el, jacobo/smart-forward.el, jacobo/smex.el, jacobo/stripe-buffer-setup.el, jacobo/yasnippet.el
ibuffer setup with ibuffer-vc.  nice ibuffer add on
removing appropriate submodules:

plugins/frame-cmds
plugins/frame-fns
plugins/org-bullets
plugins/stripe-buffer
plugins/dired-details
plugins/helm-git
plugins/markdown
plugins/magit

removed from plugins/, from .gitmodules, from .git/config, and from .git/modules/plugins/

All other removals are just folders. they were never submoduled:

ace, browse-kill-ring, expand, feature, groovy, helm, multiple, smart, smex, yas
remove helm-git deleted from configuration
auto-complete is removed completely
mark-multiple is completely removed, multiple-cursors handles this
doc-mode is gone until I need it again
grails is gone -- new grails releases make this obsolete.

levenshtein and project mode are gone which is something a backup grails mode depended on
projectile mode is gone!
deleting a lot of crap that I don't need.  Never even used some of these.  The only things that should be in plugins/ are submodules that I am working on.  spock, groovy-mode-plus, java-mode-plus, gradle-mode
gradle plugin - NOT gradle mode plugin I wrote, is now gone from repo
ignore tramp file at root
ignore multiple cursors auto generated file at root