I was about to say 'pH' but the PP got their first! Presumably as someone who is a home chutney maker, the oven drying is to help kill off any mould spores etc on the glass before filling. Also hot filling into hot jars tends to cause a vacuum and the jar lid to suck in. Not sure what is done in industry, presumably hot filling but perhaps at a hotter temperature?
control Points identified so far are:
contamination on fresh vegetables on arrival - control - washing and manual visual inspection (most veg is grown on local farms)
Some veg is prepared and delivered frozen - the factory which prepares these is audited by my friend but has a haccp process in place.
glass contamination - jars are visually inspected before and after washing and hot drying in an oven, and again before hot fill (CCP) to ensure they are intact
Wooden pallets have cardboard layers on them to prevent wooden splinters falling into jars
microbiological contamination - from plastic covering (could be rodent urine?) as pallets are brought and unpacked in the kitchen - control - good personal hygiene
metal contamination from screws in the lids of the cooking kettles - control to check they are there before putting ingredients in the kettle and during / after cooking.
The filled jars are kept in a cellar - there is the potential for contamination by pests (urine onto the jars ) so there are bait boxes and traps around the site and in the cellar.
This doesnt seem very much but it isnt a very complicated process. Is there anything else that anyone can think of?
On the fresh vegetables, as it's a manual process and it would be very difficult to identify critical limits for this, it may lend itself better to being a PRP or oPRP. Interestingly, IMO if he had an automated process, that might change due to the risk of stones with root vegetables but the chances of stones getting in are slim with manual washing and cutting.
Frozen veg sounds like a PRP for supplier control which he's doing (audits them).
Glass contamination sounds like it could possibly be a
CCP in this kind of small manufacturing site. I can see how you could get chips and cracks which could injure a consumer or cause a poor seal resulting in mould growth (potential mycotoxins?)
Wooden pallets are normally controlled in most sites I've worked in as a PRP.
Hmm, micro contamination from rat urine and the control is personal hygiene. What? Of the rats??

Seriously, if he's buying plastic from someone without a pest control contract in place he perhaps needs to reconsider his purchasing. Perhaps some supplier approval PRP (e.g. design a self assessment questionnaire for the supplier) in this case?
Personal hygiene is rarely a
CCP nowadays. Again, what is the critical limit? This lends itself naturally to be a PRP.
The cooking kettle screws I take it is an issue he's had. I'd suggest you look through the reasoning for this but if he has had an issue then it's probably a sensible approach but would be better to ensure they don't fall out easily.
I'd say if he has active rodents in a cellar he shouldn't be storing food there, even sealed food. I don't think the EHO would take a positive view. Sensible to have control but also have control around the exterior. The idea should be to prevent ingress.
Other ideas:
What about cooking temperature?
What about filling temperature? (Might be a quality thing though depending on whether mycotoxin formation is possible or likely.)
What about seal quality? (Again, probably quality but depends on the moulds likely to grow I guess?)