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You do not need to use webmaster tools and/or analytics to be found by a search engine.
But if you map your site, it is easier for them to index everything you want indexed.
Your issue may stem from some negatives that have you somewhat blacklisted or just non-indexed..
I can't tell you what they are as they could be a lot of things.
Search google and look for things that make sense to what you are doing.
Using the term blacklisting does not always describe it right but it seems what most understand even if not true.
Knowing what not to do is often more important than knowing what to do.
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