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This paper presents a modular and holistic Precision Agriculture platform, named CoFly, incorporating custom-developed AI and ICT technologies with pioneering functionalities in a UAV-agnostic system. Cognitional operations of micro Flying vehicles are utilized for data acquisition incorporating advanced coverage path planning and obstacle avoidance functionalities. Photogrammetric outcomes are extracted by processing UAV data into 2D fields and crop health maps, enabling the extraction of high-level semantic information about seed yields and quality. Based on vegetation health, CoFly incorporates a pixel-wise processing pipeline to detect and classify crop health deterioration sources. On top of that, a novel UAV mission planning scheme is employed to enable site-specific treatment by providing an automated solution for a targeted, on-the-spot, inspection. Upon the acquired inspection footage, a weed detection module is deployed, utilizing deep-learning methods, enabling weed classification. All of these capabilities are integrated inside a cost-effective and user-friendly end-to-end platform functioning on mobile devices. CoFly was tested and validated with extensive experimentation in agricultural fields with lucerne and wheat crops in Chalkidiki, Greece showcasing its performance.