Large amounts of CPU being used on mission::process_all

### Describe the bug

Exactly as it it says in the title, mission::process_all is taking up 57.74% of the total cpu, and it seems to go all the way down to item::has_flag with 43.42% of the total cpu and the highest self CPU.

I have no clue what could be causing this.

### Steps to reproduce

1. Load the save.
2. Wait for an hour and see how long it takes, or ideally profile it yourself and see that the same process is using up a large amount of cpu.

### Expected behavior

I was expecting that mission::process_all shouldn't use this much of the CPU and cause game time to crawl, but then again, what do I know?

### Screenshots


### Versions and configuration

- OS: Windows
- OS Version: 10.0.19043.2130 (21H1)
- Game Version: cca0c2b [64-bit]
- Graphics Version: Tiles
- Game Language: English [en]
- Mods loaded: [
Dark Days Ahead [dda],
Disable NPC Needs [no_npc_food],
No Fungal Growth [no_fungal_growth],
Extra Mutated Scenarios [extra_mut_scens],
Mining Mod [Mining_Mod],
SpeedyDex [speedydex],
No Rail Stations [No_Rail_Stations],
Massachusetts [MA]
]

### Additional context

Save file: https://drive.google.com/file/d/1iNm4xusioK6cGxgTYBujaYTBvSkrlo3g/view?usp=sharing

Start by profiling the reported save around mission::process_all and item::has_flag, using the issue's reproduction steps and supplied save file. Compare the hot paths with and without the listed mods to isolate the cause. Done means identifying and fixing the excessive CPU use so game time no longer crawls, with profiling evidence confirming the improvement.

Written by the indexing model from the issue text.