1- You do NOT have to do the hacking puzzles in the stages, simply talking to HQ in the comm rooms is enough to usually open the path to the boss.
2- For that matter, ALWAYS seek out a comms room first and speak with HQ, this way they can serve as checkpoints as well as unlock boss doors.
3- SFA posts have chips in them that'll allow you to access certain Areas, and while they don't offer much beyond that and a 1-up continue item, make sure to check as many rooms as you can at least.
4- In general all stages are straightforward, and may require some grappling through areas to progress. I've only included a (spoilered) note for a few just in case one gets lost.

1. Area 0- Go to the upper right section of the Area to find a door with an upgrade for the revolver, your default weapon.
2. Area 13
3. Area 5
4. Area 16
5. Area 15
6. Area 4
7. Area 1
8. Area 6
9. Area 3
10. Area 14
11. Area 8
12. Area 9
13. Area 2 Proceed through the level until you reach a dead end on the left. There would be tank on a ledge. Go the wall, Hold Down and drop a grenade to open the path to the boss below which you can reach from the path to your right from here.
Area 7
Area 18- Once you've completed Area 7, speak to the NPC next to the locked door to get the Machine Gun in the room. You can now go back to Area 7, take the lower path at the start of the stage and follow it to a hidden room. You must grapple to the right at the lowest most edge so Spencer will grab and swing onwards. Keep on this path to find the room with an upgrade for the Machine Gun.
Area 10
Area 11
Area 12

Area 19- 'Interrogate' the prisoner in order to unlock secret tunnel. These can be accessed by going between Areas 14 & 17, and 15 & 18, these reward you with the Secret Dossier and Helmet respectively.
The Helmet gives you extra defense and unlock a Medal, whereas the Dossier will inform you of a secret nearby while playing through an Area.