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Covered ranges were not merged and thus it appeared that some lines might be uncovered. To fix this I used "v8-coverage" that takes care of merging the ranges properly. With this change, coverage collected from a file by multiple entrypoints is now correctly calculated. I ended up forking https://github.com/demurgos/v8-coverage and adding "cli/tools/coverage/merge.rs" and "cli/tools/coverage/range_tree.rs".
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cover [WILDCARD]/multifile/mod.js ... 100.000% (7/7)
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