No agreement can detract from the rights and obligations provided for under the Residential Tenancies Act. Your obligation was to give the statutory period of notice of 28 or 35 days depending whether you have stayed for under 6 , or between 6-12 months. You did more than that.
A deposit is retainable for damages or other costs that you are liable for -or, sometimes, for a breach of contract that is legally valid. None of which applies.
Yes, go to PRTB and Threshold -but first do a bit of googling on the law -the websites of these two organisations are useful . Regrettably, PRTB cases can take many many months. May be worth telling the landlord - verbally and by writing after your talk - that you are taking this further.
As a landlord I'm no fan of the above organisations as they tend to act as if all landlords are wicked bloated crooks. Unfortunately, your landlord acted in a way that lends credence to that view and he deserves as much opprobrium as any tenant that acts crookedly.
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Even if it takes some time it would be interesting to hear from you as to what transpires.