Add Flowchart to repository, fix URLs in README

PrincetonUniversity · Nov 14, 2024 · 39e758a · 39e758a
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diff --git a/README.md b/README.md
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-# The Stepped Pressure Equilibrium Code
-
-All relevant publications and presentations are given on the [MRxMHD website](http://w3.pppl.gov/~shudson/Spec/spec.html).
+# The Stepped Pressure Equilibrium Code (SPEC)
 
 A BibTex file is available: [spec_refs.bib](https://raw.githubusercontent.com/PrincetonUniversity/SPEC/master/spec_refs.bib).
 
 * There is also a [brief description of SPEC](http://theory.pppl.gov/research/research.php?rid=10#h5)
   on the Princeton Plasma Physics Laboratory [Theory Department website](http://theory.pppl.gov/).
-* An overview of the algorithm is given in a [Flow Chart](http://w3.pppl.gov/~shudson/Spec/SpecFlowchart.pdf).
+* An overview of the algorithm is given in a [Flow Chart](https://princetonuniversity.github.io/SPEC/docs/SpecFlowchart.pdf).
 * Please direct questions/suggestions to [Stuart Hudson](mailto:shudson@pppl.gov?subject=spec).
-* Online documentation for SPEC is available on [Github pages](https://princetonuniversity.github.io/SPEC/).  
+* Online documentation for SPEC is available on [Github pages](https://princetonuniversity.github.io/SPEC/). 
   A PDF version of this manual is available in [SPEC_manual.pdf](https://princetonuniversity.github.io/SPEC/SPEC_manual.pdf).
-* Instructions for compiling and testing SPEC are in [Compile.md](https://github.com/PrincetonUniversity/SPEC/blob/master/Compile.md).
+* Instructions for compiling and testing SPEC are in [compilation_instructions.md](https://github.com/PrincetonUniversity/SPEC/blob/master/compilation_instructions.md).
diff --git a/docs/SpecFlowchart.pdf b/docs/SpecFlowchart.pdf