Name each file: ([a-z]+_)+[a-z]+.md where the pattern is the title.
Copy the template and fill in the sections.
Use (space separated) keywords to identify the papers.
A script (to write) will parse the domain and keyword section and make folders of symbolic links based on the parsed papers. This will result in the following layout:
./papers
./paper_1 # domain CS, keyword ml, graph
./paper_2 # domain Biology, CS keywords math, graph
./tree
./biology
./graph
./paper_2 --> ./papers/paper_2
./math
./paper_2 --> ./papers/paper_2
./cs
./ML
./paper_1 --> ./papers/paper_1
./graph
./paper_1 --> ./papers/paper_1
./paper_2 --> ./papers/paper_2
./math
./paper_2 --> ./papers/paper_2
See ./template.md