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Downloading PDFs: this is now supported for arXiv and DOI additions. ISBNs are much less trivial but I don't think Zotero/Mendeley support this either. Addition via direct Journal landing pages is planned (see here).
A final word on the comparison with papis. The major difference is the library/database structure: papis used a deeply nested library structure. Paper information gets stored in multiple info.yaml files whereas coBib was designed to use a single, centralized and plain-text (version-controlled) database file (YAML format). PDF files can be linked via paths pointing to anywhere on your filesystem (or remote URLs) which was important to me because during my studies I kept papers for various courses separate from each other.
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