Update README.md

Fixed broken manual links

Author: m-bone

README.md

@@ -1,6 +1,6 @@
 # AutoMapper
 
-AutoMapper is a package of tools designed to automate the creation of files required for the [**LAMMPS**](https://lammps.sandia.gov) command _fix bond/react_. The tools allow the user to convert LAMMPS input files into molecule format files and an automatically generated a map file of a reaction. AutoMapper will reduce these files to the smallest possible partial structure without any additional user input. AutoMapper should work with any valid LAMMPS input file, though was designed to work with [**Moltemplate**](https://github.com/jewettaij/moltemplate) output files so users may find it easier to use these packages together. AutoMapper is completely forcefield independant so users are free to use any forcefield they wish. Any problems encountered while using AutoMapper should be raised in the [**Issues**](https://github.com/m-bone/AutoMapper/issues) section where they will be addressed as quickly as possible. For a full tutorial and annotated walkthrough, see the [**manual**](https://github.com/m-bone/AutoMapper/blob/Dev-Branch/AutoMapper_Manual.pdf). An in depth overview of how AutoMapper works can be found in the [**journal article**](https://doi.org/10.1016/j.commatsci.2022.111204) in Computational Materials Science. If you use AutoMapper in your research, please cite this work in your publications. 
+AutoMapper is a package of tools designed to automate the creation of files required for the [**LAMMPS**](https://lammps.sandia.gov) command _fix bond/react_. The tools allow the user to convert LAMMPS input files into molecule format files and an automatically generated a map file of a reaction. AutoMapper will reduce these files to the smallest possible partial structure without any additional user input. AutoMapper should work with any valid LAMMPS input file, though was designed to work with [**Moltemplate**](https://github.com/jewettaij/moltemplate) output files so users may find it easier to use these packages together. AutoMapper is completely forcefield independant so users are free to use any forcefield they wish. Any problems encountered while using AutoMapper should be raised in the [**Issues**](https://github.com/m-bone/AutoMapper/issues) section where they will be addressed as quickly as possible. For a full tutorial and annotated walkthrough, see the [**manual**](https://github.com/m-bone/AutoMapper/blob/main/AutoMapper_Manual.pdf). An in depth overview of how AutoMapper works can be found in the [**journal article**](https://doi.org/10.1016/j.commatsci.2022.111204) in Computational Materials Science. If you use AutoMapper in your research, please cite this work in your publications. 
 
 AutoMapper was originally built for LAMMPS versions 29Oct20 but is being updated for new versions of REACTER. It has the capability to handle create atoms and should work with new type ID strings: both of these features were added in the 29Sept21 version. The depreciation warning caused by using `Bonding IDs` instead of `Initiator IDs` can be ignored for now. 
 
@@ -12,7 +12,7 @@ All tools are accessible through `AutoMapper.py`. They are:
 
 ## General Usage
 
-`AutoMapper.py` can be called from the command line with arguments for user control. It is recommended to put this downloaded repository on your `PATH` so that `AutoMapper.py` can be called from your modelling directories. Use `AutoMapper.py -h` for a full description of the arguments or see the [**manual**](https://github.com/m-bone/AutoMapper/blob/Dev-Branch/AutoMapper_Manual.pdf) for more details. A full [**Example Workflow**](https://github.com/m-bone/AutoMapper/tree/main/Example_Workflow) is available within the repository which walks through the use of AutoMapper within a Linux environment.
+`AutoMapper.py` can be called from the command line with arguments for user control. It is recommended to put this downloaded repository on your `PATH` so that `AutoMapper.py` can be called from your modelling directories. Use `AutoMapper.py -h` for a full description of the arguments or see the [**manual**](https://github.com/m-bone/AutoMapper/blob/main/AutoMapper_Manual.pdf) for more details. A full [**Example Workflow**](https://github.com/m-bone/AutoMapper/tree/main/Example_Workflow) is available within the repository which walks through the use of AutoMapper within a Linux environment.
 
 Below are command line examples for the different tools.