Corrected the changes as needed. Have a look if everything is okay.

I had one more doubt in mind. While working on the sketchbook refresh issue, i discovered this. In preferences if you set your sketchbook folder to some folder having large number of files (for examples sake say i set it to D: (d-drive)), then it take a lot of time for the PDE to load. That is because the addSketches method is called recursively on the directory to check if a subfolder of this folder contains sketch. Can this be called an issue?

Yes, so now you understand why we don't reload the entire sketchbook whenever a file is saved or renamed. A related issue: #2945

On new/rename/save as, only the portion of the sketchbook tree that has changed (the one file) should be updated. Re-indexing the full sketchbook is way too slow (and overkill) for that situation.

How about this:
Similar to what eclipse does...whenever we define some directory as eclipse workspace, it creates a .metadata folder from which it picks up what all projects were added to the IDE and other settings. Going on similar lines,

1. when the user is saving a program in this directory for the first time, we add the full path to the index which is stored in a separate file, that file is read only and hidden.
2. Henceforth whenever the user saves any program in this directory, it is added to the index
3. Whenever the PDE is started it can directly pick up the index from this index file. For each entry in the index file, we can check if the entry is still valid...i.e. the file has not been moved/deleted etc. (can this checking run on a separate thread so it will not slowdown the PDE loading)
4. If file is not found for some reason, ask the user if he wants to search it in the directory or knows the location in case he/she moved it.
5. Also, we keep a copy of the index file in a master folder or perform some kind of logging to retrieve entries in case index file itself is affected in that directory
6. If somehow the index file in the working directory is deleted, try and retrieve it from the master file.
7. Finally if all of above fails and user still has files in that directory, and if he/she says yes when prompted to rebuild the indexes, then call those recursive methods

(Besides, there will be other things to take care of)

Has this been already thought of before? or is there some point i am missing regarding the working of the code?

That's much too complicated, and we have always gone out of our way to avoid adding extra metadata or properties files to the sketch folder. If people want Eclipse, they should use Eclipse.

There are three things here:

1. On new/rename/save as, the entry for that sketch needs to update in the sketchbook menu. That's a regression, and needs to be fixed. sketchbook window doesn't update when sketches are added, renamed, etc #2944
2. When the sketchbook is (or even files in the current sketch are) modified outside Processing, it should automatically reload. This is handled in other pull requests, but the support is buggy so it's not turned on. PDE erroneously detects changes in non-sketch files #2759
3. Third is the performance of sketchbook loading, which should be carefully moved to an independent thread: improve start time by populating sketchbook/libraries on threads #2945

#1 is a very high priority. #2 is nice to have. #3 is also a lower priority.

Closing this one since it's out of date, it mixes several of the issues at hand (see my last comment), and also includes quite a bit of code that's not related (language, core, and even todo.txt edits).