Secret one
Find the room pictured below:
If you look at the ground in the centre of the room, you'll see it's made up of a bunch of sections - to activate this, examine the bookcases carefully - you'll see that one book sticks out a little further than the others. "use" this book
Before:
After:
and the central area of the floor opens up, forming a staircase down to a hidden underground chamber
Secret two
Find the courtyard pictured below:
The secret area is that little balcony. To get there, you first need to jump onto the banister here:
and from there onto the pillar and then to the balcony itself. The balcony has a couple of health packs.
Non-secret area
This area is pretty difficult to find, but the game doesn't credit it as an official secret.Find the courtyard pictured below. It is guarded by a couple of snipers, who shoot down from high windows.
You'll see the two short pillars beside the small staircase. Grab a chair from one of the adjoining areas, and put it onto one of these pillars (the one nearer the wall is probably the easier choice).
Then jump onto the other small pillar and from there onto the chair
from there it's a tricky but doable jump onto the porch above the door
and then onto the cornice. Once on the cornice you can walk around the courtyard, and enter each sniper's room by its window. The rooms contain a variety of weapons and health.
UPDATE:
Wombatx2754 found a much easier way up to the cornice - in the same courtyard, if you look carefully (and have the brightness/gamma setting turned up a bit) you'll notice that the downpipe near the exit has rungs on it - it's a ladder
climb it
and you'll be up on the same cornice.
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