add two index md files

docs/source/docs/fileformats_index.md

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+# Formats of Input and Output files
+
+This document the formats and examples of all the input and output
+files used in MACS3.
+
+```{toctree}
+:maxdepth: 2
+
+callpeakxls.md
+SAMBAMBAMPE.md
+BED.md
+BEDPE.md
+bedGraph.md
+narrowPeak.md
+broadPeak.md
+gappedPeak.md
+vcf.md
+hmmratacModel.md

docs/source/docs/subcommands_index.md

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+# Subcommands
+
+This section provides detailed documentation for each subcommand in
+MACS3. Use `macs3 --help` to see the list of subcommands.
+
+```{toctree}
+:maxdepth: 2
+
+callpeak.md
+callvar.md
+hmmratac.md
+bdgbroadcall.md
+bdgcmp.md
+bdgdiff.md
+bdgopt.md
+bdgpeakcall.md
+cmbreps.md
+filterdup.md
+pileup.md
+predictd.md
+randsample.md
+refinepeak.md