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There is definition of "That counts here" in online vocabularies like Merriam Webster? I can't find it.

Usage example
it is specifically the usage pattern in the code from the outside layer that counts here.

  • Compare: It's the thought that counts. That is, that "matters". – TRomano Feb 16 '19 at 12:13
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You're looking for the fourth sense of Merriam-Webster's definition of the intransitive verb count:

4 a : to have value or significance
// These are the people who really count.
// His opinions don't count for much.
b : to deserve to be regarded or considered
// a job so easy it hardly counts as work

From the thesaurus:

2 to be of importance
• punctuality and a neat appearance count during a job interview

Synonyms of COUNT
import, matter, mean, signify, weigh

Words Related to COUNT
affect, concern, influence, sway
add up (to), amount (to)

Phrases Synonymous with count
carry weight, cut ice

In other words, looking at your example sentence:

It is specifically the usage pattern in the code from the outside layer that is important here.


Note that the use of here isn't part of the meaning of count. But if you want to know what it's doing at the end of the sentence, you can replace it with in this case:

It is specifically the usage pattern in the code from the outside layer that is important in this case.

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