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Add methods:
void addLeaf(Leaf leaf);
Leaf getLeaf(long id);
void removeLeaf(Leaf id);

Remove methods:
void removeLeaf(Leaf leaf);

Same for Ground interface

Create ForestElements class and put there all strings constants used in DefaultHandler2 class

Instead of using boolean values consider following code:

int CURRENT_LEVEL = -1;
int LEVEL_TREE = 1;
int LEVEL_LEAF = 2;
....

if(CURRENT_LEVEL == LEVEL_TREE)
{
//parse tree
}
else if(CURRENT_LEVEL == LEVEL_LEAF)
{
//parse leaf
}
..

Create separate package xml and put there all classes related to xml loading.

Rename DefaultHandler2 to ForestHandler

Method endElement too big: add parseTree and parseLeaf methods

Consider following xml:

a lot of whitespace

Try to kill this whitespaces

Review this document https://gist.github.com/1561693