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Composer default directory inconsistency
#1

In config/config.php if we enable Composer by setting TRUE, CI will be looking for composer default directory in root_catalog/application/vendor.
But the default Composer catalog is root_catalog/vendor because composer.json is in root_catalog.
I suggest to add this in Composer.json:
"config": {
  "vendor-dir": "application/vendor"
},
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#2

The composer.json in CodeIgniter is used for testing, and is not meant for deployment. You need to make your own for that purpose, IIRC. It might be an idea to remove the composer.json from the release package ... I'll check with Narf.
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#3

The packaged composer.json is for CodeIgniter itself, not for your application. It would've even been excluded from releases if it wasn't required for indexing on Packagist.
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