Changes made to the moodle core code

This is a list of files in my moodle core that I have tweaked.  Moodle version 2.2.3

I am trying to use the site/local directory to house code that I have written for different things.

local/progressReportsDBFunctions.php
- contains shared functions used by both my custom reporting utilities.

local/sorter/index.php
local/sorter/SorterDB.php
local/sorter/sorterForm.php
- contain code for my gradebook item sorter utility

local/sortUtil.php
- utility for sorting the gradebook items for all the courses in the moodle

ltiprovider/
- plugin required by a vendor of ours (florida virtual) to help stream a very large course file

admin/tool/uploaduser/userform.php
- added a default selection statement, so my customer does not have to remember to choose

training/lib/filebrowser/file_info_content.php
-

report/studentprogress
- added this custom report

grade/report/progress
- added this custom report

lib/grade/grade_category.php
- vendor added function (class.com) for category

theme/styles.php
- tweaked, adding vendor rule to work with grade_category update

theme/classComPatch.php
- vendor added this style sheet for their grade category tweak

report/customsql
- this folder is a 3rd party plugin (do not think it will be effected when updating).

When updating the version of moodle, changes to the core files will be lost or overwritten anyway.  Plugins should be ok, since they are stored in the DB.  When you update a version, you are not overwriting the DB, you are replacing the code.  What you end up doing is copying the existing code infrastructure to a backup location and then removing it, while copying the new code infrastructure into place.

The updated or new code when browsed to its webroot determines that it needs to update and does about its business by reading the DB and updating it, keeping the plugins and other site settings in place.  When the site has completed its updating, you will have to manually edit the files that previously contained the tweaks.