About Safari cache and iPhoto library fragmentation...

Some days back, with the help of iDefrag I found out that my entire HD was badly fragmented inspite of having 95GBs free space. So I decided to do what an average mac user does to fix this... I backed up everything my my TM drive and restore the entire from there. Then I ran iDefrag and things were neat. A lot of my speed related issues are not solved.
However, I do notice that Safari cache and iPhoto library are always reported as fragmented portions on the HD by iDefrag. Infact, I often see the colored ball - wait indicator when switching tabs in safari or when I work with photos in iPhoto. I dont mind clearing the cache of safari. i'm somewhat worried about my iPhoto library. I have all my personal and family pics in one library as thats easier to maintain.
I just want to know what is the ideal thing for a mac user to do here...
PS: noticed that even linux virtual disk of vmware is completely fragmented, which i made after i restored with TM.

Watch your CPU usage via the +Activity Monitor+ app (in your Applications/Utilities folder).
When it starts, select either +All Processes+ or +Active Processes+ in the toolbar, and sort the list by the +% CPU+ column, so the highest numbers are on top, and select the CPU tab towards the bottom.
For this purpose, also select +View > Update Frequency > Less Often+ from the Menubar.
Various processes will "spike" up and down normally as they do things, then are idle, so you need to watch it for a while and get a feel for the processes that are using the most CPU, and the +% Idle+ at the bottom.
When the slowdown occurs, see if something changes significantly, especially if the +% idle+ goes to near zero. If that happens, see what process(es) are using the most CPU.
If the process(es) involved aren't familiar to you, post their names here (and or check this out: http://triviaware.com/macprocess/all)
You may also want to select the +System Memory+ tab towards the bottom. Keep an eye on the total of Free and Inactive memory (if they're near zero, you may need more), and the +Page outs+ (if that's high, it's another indication you may need more memory).
And see this Apple Support article: Mac OS X: Reading system memory usage in Activity Monitor

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