sat-encode: Remove unneeded include files.
sat-encode: Remove unneeded include files.

Also add comments why certain include files are needed.

ampli/link-grammar,opencog/link-grammar,ampli/link-grammar,opencog/link-grammar,MadBomber/link-grammar,linas/link-grammar,opencog/link-grammar,linas/link-grammar,ampli/link-grammar,MadBomber/link-grammar,linas/link-grammar,opencog/link-grammar,MadBomber/link-grammar,MadBomber/link-grammar,linas/link-grammar,MadBomber/link-grammar,ampli/link-grammar,linas/link-grammar,linas/link-grammar,ampli/link-grammar,linas/link-grammar,MadBomber/link-grammar,ampli/link-grammar,opencog/link-grammar,MadBomber/link-grammar,linas/link-grammar,opencog/link-grammar,opencog/link-grammar,opencog/link-grammar,linas/link-grammar,ampli/link-grammar,MadBomber/link-grammar,ampli/link-grammar,ampli/link-grammar,opencog/link-grammar