JJMC89 added a comment.

  You only need one setup.py that will install multiple site-packages. I did 
some quick testing by updating as below and things seem to work. It installs 3 
site-packages: pywikibot, pywikibot_i18n, and pywikibot_scripts.
  
    pywikibot-core
    ├── MANIFEST.in        # updated as below
    ├── pywikibot
    ├── pywikibot_i18n     # moved from ./scripts/i18n (git submodule 
pywikibot-i18n)
    ├── pywikibot_scripts  # from current ./scripts but without i18n and 
./pywikibot/scripts
    │   └── __main__.py    # moved from ./pwb.py
    ├── docs               # [git only] unchanged
    ├── maintenance        # [git only] if needed for maintenance scripts that 
should not be packaged/distributed
    ├── tests              # [git only] unchanged
    ├── pwb.py             # [git only] if needed temporarily for compatibility
    └── setup.py           # updated as below
  
  
  
    diff --git a/MANIFEST.in b/MANIFEST.in
    index 0952697fc..32cf5355a 100644
    --- a/MANIFEST.in
    +++ b/MANIFEST.in
    @@ -1 +1,2 @@
    -graft pywikibot/scripts/i18n/pywikibot
    \ No newline at end of file
    +include pywikibot_i18n/*/*.json
    +
    diff --git a/setup.py b/setup.py
    index e0e424ea5..5f15c1951 100755
    --- a/setup.py
    +++ b/setup.py
    @@ -234,7 +234,7 @@ def get_packages(name) -> List[str]:  # pragma: no cover
         except ImportError:
             sys.exit(
                 'setuptools >= 40.1.0 is required to create a new 
distribution.')
    -    packages = find_namespace_packages(include=[name + '.*'])
    +    packages = find_namespace_packages(include=[name + '*'])
         return [str(name)] + packages
    
    
    @@ -289,7 +289,7 @@ def main() -> None:  # pragma: no cover
             },
             entry_points={
                 'console_scripts': [
    -                'pwb = pywikibot.scripts.pwb:run',
    +                'pwb = pywikibot_scripts.__main__:run',
                 ],
             },
             classifiers=[

TASK DETAIL
  https://phabricator.wikimedia.org/T320851

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To: Xqt, JJMC89
Cc: Xqt, Aklapper, pywikibot-bugs-list, JJMC89, Jersione, Hellket777, 
LisafBia6531, 786, Biggs657, PotsdamLamb, Jyoo1011, JohnsonLee01, Juan90264, 
SHEKH, Dijkstra, Alter-paule, Beast1978, Un1tY, Khutuck, Zkhalido, Hook696, 
Kent7301, joker88john, Viztor, CucyNoiD, Wenyi, Gaboe420, Giuliamocci, 
Cpaulf30, Af420, Bsandipan, Tbscho, MayS, Lewizho99, Mdupont, Maathavan, 
Dvorapa, Altostratus, Neuronton, Avicennasis, mys_721tx, jayvdb, Masti, 
Alchimista
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