Fixed broken Links in readme

(Effective area, decays, SN)

README.md

@@ -78,9 +78,9 @@ sudo apt-get -y install libxerces-c-dev libxmu-dev libxpm-dev libglu1-mesa-dev q
 
 OMSim has been utilized in a range of studies, each simulating unique physics, thereby necessitating distinct Physicslist/analysis setups. In this repository, we have compiled a selection of these studies, each contained within its own folder and accompanied by its own main file. Currently available:
 
-- [Effective area](https://icecube.github.io/OMSim/md_2_effective_area.html): calculates the effective area of the optical modules/PMTs.
-- [Radioactive decays](https://icecube.github.io/OMSim/md_3_radioactive_decays.html): simulates radioactive decays within the glass of the pressure vessel and the PMT glass. Essential for understanding the primary background of optical modules. **Requires Geant4 version 11.3.0**
-- [Supernova studies](https://icecube.github.io/OMSim/md_4__s_n.html): used for the development of an improved SN trigger for IceCube using multi-PMT modules.
+- [Effective area](https://github.com/icecube/OMSim/blob/master/documentation/extra_doc/30_effective_area.md): calculates the effective area of the optical modules/PMTs.
+- [Radioactive decays](https://github.com/icecube/OMSim/blob/master/documentation/extra_doc/31_radioactive_decays.md): simulates radioactive decays within the glass of the pressure vessel and the PMT glass. Essential for understanding the primary background of optical modules. **Requires Geant4 version 11.3.0**
+- [Supernova studies](https://github.com/icecube/OMSim/blob/master/documentation/extra_doc/32_SN.md): used for the development of an improved SN trigger for IceCube using multi-PMT modules.
 
 ### Customising Compilation
 To exclude certain studies from compilation, edit the `simulations/CMakeLists.tx` file and comment out the unwanted `add_subdirectory()` calls before running CMake.