MD Example files + SVG Parser (#107)

* Jacobian.md

* Converted all examples TeX files to markdown

* added labels in front of the readme + improved link placement

* Added sphinx + GH md parser compitable author metadata

* Stable | Added linkers for the SVG format | Examples md are fully compitable for sphinx and md

* stable |  temp dump | images are being rendered over latexpdf but in lower quality

* stable | SVG+PDF generation with some warnings.

* UX improvment | Added final path linkers and pointers for doc-html

* Conducted a thorough review of the documentation and made several improvements.

* Linux PDF build fix | removed hard coded pdfmino
rversion 7 from build and readme fix

* Jacobian fix

* doc-all fix

Author: pritkc

README.md

@@ -1,5 +1,11 @@
 # MOLE: Mimetic Operators Library Enhanced
 
+[![JOSS paper][joss-badge]][joss-link]
+[![MATLAB File Exchange][matlab-badge]][matlab-link]
+[![License][license-badge]][license-link]
+[![Build Status][build-badge]][build-link]
+[![Documentation][docs-badge]][docs-link]
+
 ## Description
 
 MOLE is a high-quality (C++ & MATLAB/Octave) library that implements 
@@ -9,17 +15,10 @@ Gradient, Divergence, Laplacian, Bilaplacian, and Curl. These operators (highly
 on staggered grids (uniform, non-uniform, curvilinear) and satisfy local and 
 global conservation laws.
 
-Mathematics is based on the work of [Corbino and Castillo, 2020](https://doi.org/10.1016/j.cam.2019.06.042). 
-However, the user may find helpful previous publications, such as [Castillo and Grone, 2003](https://doi.org/10.1137/S0895479801398025),
+Mathematics is based on the work of [Corbino and Castillo][corbino-paper]. 
+However, the user may find helpful previous publications, such as [Castillo and Grone][castillo-paper],
 in which similar operators were derived using a matrix analysis approach.
 
-
-## Licensing
-
-MOLE is distributed under a GNU General Public License; please refer to the _LICENSE_ 
-file for more details.
-
-
 ## Installation
 
 ### Prerequisites
@@ -32,7 +31,7 @@ To install the MOLE library, you'll need the following packages:
 - LAPACK (Mac only)
 - libomp (Mac only)
 
-For documentation build requirements, please refer to the [Documentation Guide](doc/sphinx/README.md).
+For documentation build requirements, please refer to the [Documentation Guide][doc-guide].
 
 ### Package Installation by OS
 
@@ -45,7 +44,7 @@ sudo apt install cmake libopenblas-dev libeigen3-dev
 
 #### macOS Systems
 
-Install [Homebrew](https://brew.sh/) if you don't have it already, then run:
+Install [Homebrew][homebrew] if you don't have it already, then run:
 
 ```bash
 # Install all required packages
@@ -70,7 +69,7 @@ brew install cmake openblas eigen libomp lapack
 sudo yum install cmake openblas-devel eigen3-devel
 ```
 
-### Building and Installing MOLE
+## Building and Installing
 
 1. Clone the repository:
    ```bash
@@ -101,40 +100,50 @@ sudo yum install cmake openblas-devel eigen3-devel
 
 **Note:** Armadillo and SuperLU will be automatically installed in the build directory during the build process.
 
+## Testing
 
-## Examples and Tests
+### C++ 
 
-MOLE provides comprehensive examples and tests for both C++ and MATLAB/Octave implementations to help you get started quickly.
+A suite of four automatic tests that verify MOLE's installation and dependencies. These tests run automatically during the C++ library construction.
 
-### Available Resources
+Run from the `build` directory:
+```bash
+make run_tests
+```
 
-#### Tests
-- **tests/cpp**:
-  A suite of four automatic tests that verify MOLE's installation and dependencies. These tests run automatically during the C++ library construction.
-  - Run: `make run_tests` in the build directory
+### MATLAB/Octave 
 
-- **tests/matlab**:
-  MATLAB/Octave equivalent of the C++ test suite. We recommend running these tests before using MOLE to ensure proper setup.
-  - Run: Navigate to `tests/matlab` and execute `run_tests.m`
+MATLAB/Octave equivalent of the C++ test suite. We recommend running these tests before using MOLE to ensure proper setup.
 
-#### Examples
-- **examples/cpp**:
-  Four self-contained, well-documented examples demonstrating typical PDE solutions. These are automatically built with `make` and serve as an excellent starting point for C++ users.
+Run from the `tests/matlab`:
+```matlab
+run_tests
+```
 
-- **examples/matlab**:
-  A collection of over 30 examples showcasing various PDE solutions, from simple linear one-dimensional problems to complex nonlinear multidimensional scenarios.
+## Examples
 
-We recommend running the tests before starting to use the library to ensure everything is working correctly.
+### C++ 
+
+Four self-contained, well-documented examples demonstrating typical PDE solutions. These are automatically built with `make` and serve as an excellent starting point for C++ users.
+
+### MATLAB/Octave Examples
+
+A collection of over 30 examples showcasing various PDE solutions, from simple linear one-dimensional problems to complex nonlinear multidimensional scenarios.
 
 ## Documentation
 
 MOLE comes with comprehensive documentation:
 
-- **API Reference & User Guide**: Access our online [Documentation](https://csrc-sdsu.github.io/mole/build/html/)
-- **Building Documentation**: To build documentation locally, follow our [Documentation Build Guide](doc/sphinx/README.md)
+- **API Reference & User Guide**: Access our online [Documentation][docs-link]
+- **Building Documentation**: To build documentation locally, follow our [Documentation Guide][doc-guide].
 
 > **Important Note:** Performing non-unary operations involving operands constructed over different grids may lead to unexpected results. While MOLE allows such operations without throwing errors, users must exercise caution when manipulating operators across different grids.
 
+## Licensing
+
+MOLE is distributed under a GNU General Public License; please refer to the _LICENSE_ 
+file for more details.
+
 ## Community Guidelines
 
 We welcome contributions to MOLE, including:
@@ -144,16 +153,12 @@ We welcome contributions to MOLE, including:
 - Reporting bugs
 - Requesting new features
 
-Please refer to our [Contribution Guidelines](https://github.com/csrc-sdsu/mole/blob/master/CONTRIBUTING.md) for more details.
-
+Please refer to our [Contribution Guidelines][contrib-guide] for more details.
 
 ## Citations
 
 Please cite our work if you use MOLE in your research or software. 
-Citations are helpful for the continued development and maintenance of 
-the library [![DOI](doc/assets/img/joss-status.svg)](https://doi.org/10.21105/joss.06288)
-
-[![View mole on File Exchange](doc/assets/img/matlab-file-exchange.svg)](https://www.mathworks.com/matlabcentral/fileexchange/124870-mole)
+Citations are helpful for the continued development and maintenance of the library.
 
 ## Gallery
 
@@ -166,4 +171,22 @@ Now, some cool pictures obtained with MOLE:
 ![Obtained with curvilinear operators](doc/assets/img/grid.png)
 ![Obtained with curvilinear operators](doc/assets/img/WavyGrid.png)
 ![Obtained with curvilinear operators](doc/assets/img/wave2D.png)
-![Obtained with curvilinear operators](doc/assets/img/burgers.png)
+![Obtained with curvilinear operators](doc/assets/img/burgers.png)
+
+<!-- Link references -->
+
+[joss-badge]: https://joss.theoj.org/papers/10.21105/joss.06288/status.svg
+[joss-link]: https://doi.org/10.21105/joss.06288
+[matlab-badge]: https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg
+[matlab-link]: https://www.mathworks.com/matlabcentral/fileexchange/124870-mole
+[license-badge]: https://img.shields.io/badge/License-GPLv3-blue.svg
+[license-link]: https://www.gnu.org/licenses/gpl-3.0
+[build-badge]: https://img.shields.io/github/actions/workflow/status/csrc-sdsu/mole/cmake.yml?branch=master&label=Build
+[build-link]: https://github.com/csrc-sdsu/mole/actions
+[docs-badge]: https://img.shields.io/badge/docs-latest-brightgreen.svg
+[docs-link]: https://csrc-sdsu.github.io/mole/build/html/
+[corbino-paper]: https://doi.org/10.1016/j.cam.2019.06.042
+[castillo-paper]: https://doi.org/10.1137/S0895479801398025
+[doc-guide]: https://github.com/csrc-sdsu/mole/blob/master/doc/sphinx/README.md
+[homebrew]: https://brew.sh/
+[contrib-guide]: https://github.com/csrc-sdsu/mole/blob/master/CONTRIBUTING.md