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if (this.lastPkgFragmentRootPath == null || !(resourcePath.startsWith(this.lastPkgFragmentRootPath) && (rootPathLength = this.lastPkgFragmentRootPath.length()) > 0 && resourcePath.charAt(rootPathLength) == '/')) { The above check is faulty because in JSDT, unlike JDT, it is possible to have a library container as a child of a source folder. The lastPkgFragmentRootPath was getting screwed up and resulting in the incorrect creation of package fragments.
Created attachment 172365 [details] patch
Patch checked in.