Disclaimer: I am not a developer of the game. My notes below come from my experiences and gameplay, as well as those of others. I will try to keep this as up to date as possible, as new patches come out or changes are made.
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If ever there was a basic-bitch ghost, the Spirit is it. With no "official" strenghts or weaknesses, this ghost can be difficult to identify without all 3 evidences.
My best advice: use the smudge timer test. The Spirit cannot hunt until 3 minutes (180 seconds) after being smudged. Comparatively, all other ghosts (besides Demon) can hunt 90 seconds after being smudged. (Demon is only 60 seconds.)
To smudge the ghost, I recommend lighting the smudge DURING a hunt and starting the timer then. Smudging during a hunt will count as smudging the ghost no matter where you or the ghost is located at the time. If you smudge while the ghost is not hunting, you will need to make sure you are in close proximity to the ghost.
Test: Smudge the ghost during a hunt and start timing. If the ghost attempts to hunt (starts a hunt or burns a crucifix) before 180 seconds are up, you can rule out Spirit.
Note that this test rules out a Spirit, but does not necessarily guarantee that it IS a Spirit if it hunts after 180 seconds. If you get the same results (only hunts AFTER 180 seconds after smudge), conclusively, it is more likely to be a Spirit.
When I try to trust my instincts, this ghost can feel like so many other ghosts. I just have to rely on the test.
Evidences:
EMF 5
Spirit Box
Ghost Writing
Other tips of note:
Smudging
Once a smudge is lit during a hunt, the game initiates its own timer. If another smudge is lit while this timer is still active, the timer will NOT reset. The game will continue using the timer of the first smudge.
For example: you light a smudge 5 seconds into a hunt. Someone else on your team then lights a smudge 10 seconds later during the same hunt because they need to escape. That means the second smudge was lit while the timer of the first smudge was still active. You know this because the minimum amount of time that a smudge lasts if lit during a hunt is 60 seconds (for a Demon), but can be 90 seconds (other ghosts) or even 180 seconds (Spirit). The timer you should be using for these tests will be from the FIRST smudge.
This is information I obtained from high level Phas streamers who have connections to the developers. I have not personally tested this extensively.
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If you have comments or think I have something incorrect/missing, please do comment on the blog for discussion. I'd like to keep these pages as accurate and up to date as possible.