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(Co)chain complexes, abelian Categories, (pre)sheaves, (co)homology in various (possibly highly generalized) settings, spectra, derived functors, resolutions, spectral sequences, homotopy categories. Chain complexes in an abelian category form the heart of homological algebra.
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Projective dimension
Counterexamples can even be found in a domain, by taking rings of higher dimension or singular rings—once you're no longer over a PID, ideals will suffice. Take $R = k[x,y]$, the module $M = R$ itsel …