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You probably need to differentiate thinking and thought.
Intent is kamma. One executes intent through thinking, speaking and doing (physical action).
Thought is vinnana, which is defined as "to especially know".
A thought will not arise without matter & state's of matter (rupa), sensations (vedana), recognitions (sanna), intents (sankara, kamma).
Another thing to note is manasikara, which means "to direct attention".
Thoughts are generally considered external similar to visions, sounds, odours, tastes, physical sensations.
Thinking is considered internal, generally.
Generally - I use the word generally here because in dhamma, having a view of a self that is permanent (soul) is a delusion, hence both thinking and thought does not belong to a permanent self (soul), thus not well defined as internal or external. In fact, a person without proper view is known to delude one self in 20 ways: that rupa, vedana, sanna, sankara, vinna x is me, I'm made of them, they are inside me, I'm inside them. By all 20 such combinations, one arrives at a false view of a self. This, you can now match with Freuds ego and super ego. I can provide references from pali canon if you need.
Don't take my word for it though, research on the italicised words above, which are pali.
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I would like to second SaranthW's suggestion with a link to an extensive Āryavasubandho Abhidharmakośakārikā commentary:
https://abhidharmakosa.files.wordpress.com/2010/09/kosa-karika-study.pdf
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where does thought come from? depends on the definition of thought. i tend to think of a thought as idea. the recognition of that idea gives way to verbalization - both by speech and internal. internal speech may only be somewhere on a spectrum of thinking. that i won't develop here since I am not too familiar.
the buddha says in A 6.63 Nibbedhika Sutta Penetrative:
"And what is the result of perception? Perception has communication by speech as its result, I tell you. However a person perceives something, that is how he expresses it: 'I have this sort of perception.' This is called the result of perception.
self-awareness is also definition. Questioning the existence of self leading to insight, or some knowledge of the truth.
It's possible to dismiss the thought, but that depends on how much value,attachment you give to that particular thought, idea.
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I find it useful here to distinguish between a thought and an attitude. An attitude is like a mental posture towards the world: a way of orienting oneself within the flow and context of what surrounds us. A thought, by contrast, is an action: a way of wrestling with, addressing, correcting, or adjusting (etc) something. If we think about a sailing ship and its crew, a ship lies a certain way with respect to the wind and the water (its attitude), and then the captain issues an order (a thought) which starts a process that may ultimately changes the attitude of the ship.
In this sense, an insight is a change in attitude, something which alters the deportment of the self holistically, while a thought is a momentary arising meant to deal with some practical issue.
Now, most people in the world have fragmented and inconsistent attitudes, a general sense of being 'off balance' or 'out of kilter'. They do well enough by using the power of thought to keep things in line, constantly controlling or adjusting the world around them to keep themselves in their comfort zone while occasionally getting the rug pulled out from under them and having to spasmodically pick themselves up again. That's the dance of karma... But Buddhism (and every spiritual tradition, for that matter) tries to get people to integrate their attitude — to have one attitude that works for everything — so that the need to adjust and control the world dissipates. If you want to use the programmer/program metaphor (which I generally dislike) then the goal is to craft a program that the programmer doesn't constantly have to tweak and fix. We want a program that runs without crashing, freezing, hiccups, or weird outputs, no matter what inputs it faces, so that we can free our mind from the constant struggle and worry of maintaining it.
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According to Buddhism thought to arise from the consciousness. Which are called Vitakka and Vicara. There are many types of wholesome and unwholesome thoughts. A person should have a good grasp of Abhidhamma to understand the differences completely.
Abhidhamma in practice: http://103.242.110.22/theravadins/English-articles/abhidhamma-in-practice.pdf