difference between site:domain.com & site:domain.com/directory?

Whats the difference between scraping; site:domain.com & site:domain.com/directory?

Does scraping the 'root' directory gives you more internal links?

i have problems with this anyway .....
if i scrape a domain
site:www.xyz.com
custom footprint and no KW

ist harvest the pages and when ready removes everything except of one with the message to many similar KW used ..........

but i did not use any .....so what is wrong.
if i scrape like that no result.

scraping domain.com will give you more site links
coz it includes domain.com /directory1 domain.com/directory2
it will include all the directories listed by particular SE