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I'd like to propose as a solution to this, having a .splignore file, similar to something like .gitignore, which we read to determine what files/folders should be excluded from the build archive. We could by default, if the file is not found, exclude your suggestions above. As a future enhancement, when we add functionality for a "new spl application" wizard or similar, we could pre-populate a .splignore file with what the "default" set of ignored files/folders. I feel this would be a safer approach than ignoring multiple directories that a user could potentially have need of for their build.
There's extra stuff being put in the build archive that is not needed at compile time and bloats the build archive.
When topology creates a build archive it excludes these items from a toolkit (relative to the root):
toolkit.xml
doc
output
samples
opt/client
https://github.com/IBMStreams/streamsx.topology/blob/c522e24e4ad954ad7acb88b29d023b86a07dc04a/java/src/com/ibm/streamsx/topology/internal/context/remote/ZippedToolkitRemoteContext.java#L227
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