OSI Codes Inc. Coding Standard (brief description)
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All SQL queries are called by function APIs and NEVER
within the code.  This keeps the code clean and organized
so you know exactly what function does what.  And if the
database is changed, you simply change the function, not
the code.

Once you look into the API directory, you will see how we
organize our codes that calls the database.  Since data
is most important, our APIs are highly organized functions,
all within their respective files:

get.php - all sql queries that "gets" the data from db
put.php, - sql queries that "puts" into the db
remove.php - sql queries that deletes from the db
update.php. - you get the point...

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versions flags:
setup/index.php
setup/options.php
seteup/patches/index.php