Update README.md

Updated the main readme to avoid duplicating data in the examples to achieve better readability.

README.md

@@ -9,9 +9,39 @@ which is used to create a virtual network topology by using FreeBSD
 All presented scenarios run on in the IMUNES virtual machine that can be
 downloaded from: http://www.imunes.net/dl/IMUNES_security.ova.
 
+The IMUNES manual is located [here](http://imunes.net/dl/imunes_user_guide.pdf).
+
 To run the scenarios, after starting the virtual machine, just git pull the latest
 version of the repository in /root/imunes-security:
 ```
 # cd imunes-security
 # git pull
 ```
+## Starting experiments in IMUNES
+From shell:
+```
+# imunes -b mitm.imn
+```
+or from GUI:
+```
+# imunes mitm.imn
+```
+and then select the menu *Experiment -> Execute*.
+
+## Executing commands in virtual nodes
+From shell (with the [himage](http://imunes.tel.fer.hr/trac/wiki/WikiImunesExamples#himage) command):
+```
+# himage node_name command
+```
+or from GUI:
+* double-click on a virtual node in a running experiment
+* right-click on a virtual node and select *Shell window -> csh* or *Shell window -> bash*
+
+## Copying files from and to virtual nodes
+This can be done only from shell by using the [hcp](http://imunes.tel.fer.hr/trac/wiki/WikiImunesExamples#hcp) command:
+```
+# hcp script.py node_name:
+# hcp node_name:script.log .
+# hcp n0:key.pem n1:
+```
+