Use qualified module names and coqc -Q instead of -R.

SConstruct

@@ -3,7 +3,7 @@
 import os, glob, string
 
 modules = ["prelude", "iris"]
-Rs = '-R . iris'
+Rs = ' '.join(['-Q ' + x + ' ' + x for x in modules])
 env = DefaultEnvironment(ENV = os.environ,tools=['default', 'Coq'], COQFLAGS=Rs)
 
 # Coq dependencies
@@ -15,4 +15,4 @@ ParseDepends('deps')
 for v in vs: env.Coq(v)
 
 # Coqidescript
-env.CoqIdeScript('coqidescript', [])
+env.CoqIdeScript('coqidescript', [], COQFLAGS=Rs)

iris/agree.v

-Require Export cmra.
+Require Export iris.cmra.
 Local Hint Extern 10 (_ ≤ _) => omega.
 
 Record agree A `{Dist A} := Agree {

iris/auth.v

-Require Export excl.
+Require Export iris.excl.
 Local Arguments disjoint _ _ !_ !_ /.
 Local Arguments included _ _ !_ !_ /.
 

iris/cmra.v

-Require Export ra cofe cofe_instances.
+Require Export iris.ra iris.cofe.
 
 Class ValidN (A : Type) := validN : nat → A → Prop.
 Instance: Params (@validN) 3.

iris/cofe.v

-Require Export prelude.
+Require Export prelude.prelude.
 Obligation Tactic := idtac.
 
 (** Unbundeled version *)

iris/cofe_instances.v

-Require Export cofe.
-Require Import fin_maps pmap nmap zmap stringmap.
+Require Export iris.cofe.
+Require Import prelude.fin_maps prelude.pmap prelude.nmap prelude.zmap prelude.stringmap.
 
 (** Discrete cofe *)
 Section discrete_cofe.

iris/cofe_solver.v

-Require Export cofe.
+Require Export iris.cofe.
 
 Section solver.
 Context (F : cofeT → cofeT → cofeT).

iris/dra.v

-Require Export ra.
+Require Export iris.ra.
 
 (** From disjoint pcm *)
 Record validity {A} (P : A → Prop) : Type := Validity {

iris/excl.v

-Require Export cmra.
+Require Export iris.cmra.
 Local Arguments disjoint _ _ !_ !_ /.
 Local Arguments included _ _ !_ !_ /.
 

iris/logic.v

-Require Import cmra cofe_instances.
+Require Import iris.cmra.
 Local Hint Extern 1 (_ ≼ _) => etransitivity; [eassumption|].
 Local Hint Extern 1 (_ ≼ _) => etransitivity; [|eassumption].
 Local Hint Extern 10 (_ ≤ _) => omega.

iris/ra.v

-Require Export collections relations.
+Require Export prelude.collections prelude.relations.
 
 Class Valid (A : Type) := valid : A → Prop.
 Instance: Params (@valid) 2.

iris/sts.v

-Require Export ra.
-Require Import sets stringmap dra.
+Require Export iris.ra.
+Require Import prelude.sets prelude.stringmap iris.dra.
 Local Arguments valid _ _ !_ /.
 Local Arguments op _ _ !_ !_ /.
 Local Arguments unit _ _ !_ /.

prelude/assoc.v

@@ -6,8 +6,8 @@ main advantage of these association lists compared to search trees, is that it
 has canonical representatives and thus extensional Leibniz equality. Compared
 to a naive unordered association list, the merge operation (used for unions,
 intersections, and difference) is also linear-time. *)
-Require Import mapset.
-Require Export fin_maps.
+Require Import prelude.mapset.
+Require Export prelude.fin_maps.
 
 (** Because the association list is sorted using [strict lexico] instead of
 [lexico], it automatically guarantees that no duplicates exist. *)

prelude/collections.v

@@ -3,7 +3,7 @@
 (** This file collects definitions and theorems on collections. Most
 importantly, it implements some tactics to automatically solve goals involving
 collections. *)
-Require Export base tactics orders.
+Require Export prelude.base prelude.tactics prelude.orders.
 
 Instance collection_subseteq `{ElemOf A C} : SubsetEq C := λ X Y,
   ∀ x, x ∈ X → x ∈ Y.

prelude/countable.v

 (* Copyright (c) 2012-2015, Robbert Krebbers. *)
 (* This file is distributed under the terms of the BSD license. *)
-Require Export list.
+Require Export prelude.list.
 Local Obligation Tactic := idtac.
 Local Open Scope positive.
 

prelude/decidable.v

@@ -3,7 +3,7 @@
 (** This file collects theorems, definitions, tactics, related to propositions
 with a decidable equality. Such propositions are collected by the [Decision]
 type class. *)
-Require Export proof_irrel.
+Require Export prelude.proof_irrel.
 
 Hint Extern 200 (Decision _) => progress (lazy beta) : typeclass_instances.
 

prelude/error.v

 (* Copyright (c) 2012-2015, Robbert Krebbers. *)
 (* This file is distributed under the terms of the BSD license. *)
-Require Export list.
+Require Export prelude.list.
 
 Definition error (S E A : Type) : Type := S → E + (A * S).
 

prelude/fin_collections.v

@@ -3,8 +3,8 @@
 (** This file collects definitions and theorems on finite collections. Most
 importantly, it implements a fold and size function and some useful induction
 principles on finite collections . *)
-Require Import Permutation relations listset.
-Require Export numbers collections.
+Require Import Permutation prelude.relations prelude.listset.
+Require Export prelude.numbers prelude.collections.
 
 Instance collection_size `{Elements A C} : Size C := length ∘ elements.
 Definition collection_fold `{Elements A C} {B}

prelude/fin_map_dom.v

@@ -3,7 +3,7 @@
 (** This file provides an axiomatization of the domain function of finite
 maps. We provide such an axiomatization, instead of implementing the domain
 function in a generic way, to allow more efficient implementations. *)
-Require Export collections fin_maps.
+Require Export prelude.collections prelude.fin_maps.
 
 Class FinMapDom K M D `{FMap M,
     ∀ A, Lookup K A (M A), ∀ A, Empty (M A), ∀ A, PartialAlter K A (M A),

prelude/fin_maps.v

@@ -5,7 +5,7 @@ finite maps and collects some theory on it. Most importantly, it proves useful
 induction principles for finite maps and implements the tactic
 [simplify_map_equality] to simplify goals involving finite maps. *)
 Require Import Permutation.
-Require Export relations vector orders.
+Require Export prelude.relations prelude.vector prelude.orders.
 
 (** * Axiomatization of finite maps *)
 (** We require Leibniz equality to be extensional on finite maps. This of