in reply to What is your Javascript-workflow?
I maintain the two files separately ... and for the Javascript portion of the system I now prefer to write in the haXe programming language, using it to generate Javascript. The essential difference is that haXe is a strongly-typed language that can produce compile-time errors... and it is cross-platform. Definitely something to keep on your radar...
All web-page outputs are generated by templates, and those (usually, the wrappers) deliver the JavaScript by script-reference tags to external files. I basically do not use in-line (script-tag) JS content.
I use an editor (Eclipse) which is capable of both Perl and JavaScript syntax-checking ... JSLint and more ... but it cannot handle a file that consists of more-than-one language.