To add to what fieldstone said:
The foundation would probably want to feed this plants periodically, they don't want it to starve to death. A sentence or two in the containment procedures could address this without upsetting the flow.
All types of plant-based materials, including wood, natural rubber and plant-based fibers were removed from the chamber and replaced with synthetic alternatives.
The use of the word "were" in this sentence is weird. The ConProcs are instructions, not descriptions of past events. I'd replace "were" with "are to be."
which were later confirmed to act as either Greenfly- or Locust- class botanical cognitohazards.
This needs serious elaboration, because I don't know what the heck a "botanical cognitohazard" is. I struggle to even imagine how the adjective "botanical" could be applied to a cognitohazard.
Overall, this has some nice imagery, but I agree with fieldstone that it could use some more conceptual cohesion. I wouldn't take out the D-Class eating the fruit, as I liked some of the imagery there, but I would shorten that section. Also, while reading the segment describing the carving, I struggled to understand whether the entity wanted to help or harm the human. Are the vines trying to break the chains, or make them stronger? The article doesn't say anything about how the entity responds to humans, so I'm left feeling like I'm missing something.