diff --git a/scripts/nix-build.in b/scripts/nix-build.in
index a5d747686..5ae591f35 100644
--- a/scripts/nix-build.in
+++ b/scripts/nix-build.in
@@ -23,7 +23,7 @@ for i in "$@"; do
             for j in $storeExprs; do
                 echo "store expression is $j" >&2
             done
-            outPaths=$(@bindir@/nix-store -qnfv $extraArgs $storeExprs)
+            outPaths=$(@bindir@/nix-store -rv $extraArgs $storeExprs)
             for j in $outPaths; do
                 echo "$j"
                 if test -z "$noLink"; then
diff --git a/scripts/nix-collect-garbage.in b/scripts/nix-collect-garbage.in
index 44bcc16bb..f11ed2cb6 100644
--- a/scripts/nix-collect-garbage.in
+++ b/scripts/nix-collect-garbage.in
@@ -9,7 +9,6 @@ my $storeDir = "@storedir@";
 my %alive;
 
 my $gcOper = "--delete";
-my $minAge = 0;
 
 my @roots = ();
 
@@ -20,33 +19,11 @@ for (my $i = 0; $i < scalar @ARGV; $i++) {
     if ($arg eq "--delete" || $arg eq "--print-live" || $arg eq "--print-dead") {
         $gcOper = $arg;
     }
-    elsif ($arg eq "--min-age") {
-        $i++;
-        $minAge = undef;
-        $minAge = $ARGV[$i];
-        die "invalid minimum age" unless defined $minAge && $minAge =~ /^\d*$/;
-    }
     else { die "unknown argument `$arg'" };
 }
 
 
-# Read all GC roots from the given file.
-sub readRoots {
-    my $fileName = shift;
-    open ROOT, "<$fileName" or die "cannot open `$fileName': $!";
-    while (<ROOT>) {
-        chomp;
-        foreach my $root (split ' ') {
-            die "bad root `$root' in file `$fileName'"
-                unless $root =~ /^\S+$/;
-            push @roots, $root;
-        }
-    }
-    close ROOT;
-}
-
-
-# Recursively finds all *.gcroot files in the given directory.
+# Recursively finds all symlinks to the store in the given directory.
 sub findRoots;
 sub findRoots {
     my $followSymlinks = shift;
@@ -58,14 +35,26 @@ sub findRoots {
 
     foreach my $name (@names) {
         next if $name eq "." || $name eq "..";
-        $name = $dir . "/" . $name;
-        if ($name =~ /.gcroot$/ && -f $name) {
-            readRoots $name;
-        }
-        elsif (-d $name) {
-            if ($followSymlinks || !-l $name) {
-                findRoots 0, $name;
+        my $path = $dir . "/" . $name;
+
+        if (-l $path) {
+            my $target = readlink $path
+                or die "cannot read symlink `$path': $!";
+            
+            if (substr($target, 0, length $storeDir) eq $storeDir) {
+                # We're only interested in the store-level part.
+                $target = substr($target, length $storeDir);
+                $target = "$storeDir/$target";
+                push @roots, $target;
             }
+
+            elsif ($followSymlinks && -d $path) {
+                findRoots 0, $path;
+            }
+        }
+        
+        elsif (-d $path) {
+            findRoots $followSymlinks, $path;
         }
     }
     
@@ -77,7 +66,7 @@ findRoots 1, $rootsDir;
 
 
 # Run the collector with the roots we found.
-my $pid = open2(">&1", \*WRITE, "@bindir@/nix-store --gc $gcOper --min-age $minAge")
+my $pid = open2(">&1", \*WRITE, "@bindir@/nix-store --gc $gcOper")
     or die "cannot run `nix-store --gc'";
 
 foreach my $root (@roots) {
diff --git a/src/libstore/build.cc b/src/libstore/build.cc
index b63488b8d..52bd08bb1 100644
--- a/src/libstore/build.cc
+++ b/src/libstore/build.cc
@@ -458,7 +458,7 @@ void DerivationGoal::haveStoreExpr()
          i != invalidOutputs.end(); ++i)
         /* Don't bother creating a substitution goal if there are no
            substitutes. */
-        if (querySubstitutes(*i).size() > 0)
+        if (querySubstitutes(noTxn, *i).size() > 0)
             addWaitee(worker.makeSubstitutionGoal(*i));
 
     if (waitees.empty()) /* to prevent hang (no wake-up event) */
@@ -1315,7 +1315,7 @@ void SubstitutionGoal::init()
     }
 
     /* Read the substitutes. */
-    subs = querySubstitutes(storePath);
+    subs = querySubstitutes(noTxn, storePath);
 
     /* To maintain the closure invairant, we first have to realise the
        paths referenced by this one. */
diff --git a/src/libstore/gc.cc b/src/libstore/gc.cc
index 4f3306505..ba6e6bb9d 100644
--- a/src/libstore/gc.cc
+++ b/src/libstore/gc.cc
@@ -1,12 +1,68 @@
 #include "globals.hh"
 #include "gc.hh"
-
+#include "build.hh"
 
 #include <sys/types.h>
 #include <sys/stat.h>
 #include <unistd.h>
 
 
+void collectGarbage(const PathSet & roots, GCAction action,
+    PathSet & result)
+{
+    result.clear();
+    
+    /* !!! TODO: Acquire an exclusive lock on the gcroots directory.
+       This prevents the set of live paths from increasing after this
+       point. */
+    
+    /* Determine the live paths which is just the closure of the
+       roots under the `references' relation. */
+    PathSet livePaths;
+    for (PathSet::const_iterator i = roots.begin(); i != roots.end(); ++i)
+        computeFSClosure(canonPath(*i), livePaths);
+
+    if (action == gcReturnLive) {
+        result = livePaths;
+        return;
+    }
+
+    /* !!! TODO: Try to acquire (without blocking) exclusive locks on
+       the files in the `pending' directory.  Delete all files for
+       which we managed to acquire such a lock (since if we could get
+       such a lock, that means that the process that owned the file
+       has died). */
+
+    /* !!! TODO: Acquire shared locks on all files in the pending
+       directories.  This prevents the set of pending paths from
+       increasing while we are garbage-collecting.  Read the set of
+       pending paths from those files. */
+
+    /* Read the Nix store directory to find all currently existing
+       paths. */
+    Strings storeNames = readDirectory(nixStore);
+
+    for (Strings::iterator i = storeNames.begin(); i != storeNames.end(); ++i) {
+        Path path = canonPath(nixStore + "/" + *i);
+
+        if (livePaths.find(path) != livePaths.end()) {
+            debug(format("live path `%1%'") % path);
+            continue;
+        }
+
+        debug(format("dead path `%1%'") % path);
+        result.insert(path);
+
+        if (action == gcDeleteDead) {
+            printMsg(lvlInfo, format("deleting `%1%'") % path);
+            deleteFromStore(path);
+        }
+        
+    }
+}
+
+
+
 #if 0
 void followLivePaths(Path nePath, PathSet & live)
 {
diff --git a/src/libstore/gc.hh b/src/libstore/gc.hh
index d1ca5c63e..2ea851abc 100644
--- a/src/libstore/gc.hh
+++ b/src/libstore/gc.hh
@@ -3,24 +3,15 @@
 
 #include "util.hh"
 
+/* Garbage collector operation. */
+typedef enum { gcReturnLive, gcReturnDead, gcDeleteDead } GCAction;
 
-/* Determine the set of "live" store paths, given a set of root store
-   expressions.  The live store paths are those that are reachable
-   from the roots.  The roots are reachable by definition.  Any path
-   mentioned in a reachable store expression is also reachable.  If a
-   derivation store expression is reachable, then its successor (if it
-   exists) if also reachable.  It is not an error for store
-   expressions not to exist (since this can happen on derivation store
-   expressions, for instance, due to the substitute mechanism), but
-   successor links are followed even for non-existant derivations. */
-PathSet findLivePaths(const Paths & roots);
-
-/* Given a set of "live" store paths, determine the set of "dead"
-   store paths (which are simply all store paths that are not in the
-   live set).  The value `minAge' specifies the minimum age in seconds
-   for an unreachable file to be considered dead (0 meaning that any
-   unreachable file is dead). */
-PathSet findDeadPaths(const PathSet & live, time_t minAge);
-
+/* If `action' is set to `soReturnLive', return the set of paths
+   reachable from (i.e. in the closure of) the specified roots.  If
+   `action' is `soReturnDead', return the set of paths not reachable
+   from the roots.  If `action' is `soDeleteDead', actually delete the
+   latter set. */
+void collectGarbage(const PathSet & roots, GCAction action,
+    PathSet & result);
 
 #endif /* !__GC_H */
diff --git a/src/libstore/store.cc b/src/libstore/store.cc
index f5e7d2aa5..30573992c 100644
--- a/src/libstore/store.cc
+++ b/src/libstore/store.cc
@@ -363,9 +363,9 @@ void registerSubstitute(const Transaction & txn,
 }
 
 
-Substitutes querySubstitutes(const Path & srcPath)
+Substitutes querySubstitutes(const Transaction & txn, const Path & srcPath)
 {
-    return readSubstitutes(noTxn, srcPath);
+    return readSubstitutes(txn, srcPath);
 }
 
 
@@ -411,6 +411,13 @@ static void invalidatePath(const Path & path, Transaction & txn)
     debug(format("unregistering path `%1%'") % path);
 
     nixDB.delPair(txn, dbValidPaths, path);
+
+    /* Clear the `references' entry for this path, as well as the
+       inverse `referers' entries; but only if there are no
+       substitutes for this path.  This maintains the cleanup
+       invariant. */
+    if (querySubstitutes(txn, path).size() == 0)
+        setReferences(txn, path, PathSet());
 }
 
 
diff --git a/src/libstore/store.hh b/src/libstore/store.hh
index 968786305..dce4eb1d6 100644
--- a/src/libstore/store.hh
+++ b/src/libstore/store.hh
@@ -45,7 +45,7 @@ void registerSubstitute(const Transaction & txn,
     const Path & srcPath, const Substitute & sub);
 
 /* Return the substitutes for the given path. */
-Substitutes querySubstitutes(const Path & srcPath);
+Substitutes querySubstitutes(const Transaction & txn, const Path & srcPath);
 
 /* Deregister all substitutes. */
 void clearSubstitutes();
diff --git a/src/nix-env/main.cc b/src/nix-env/main.cc
index 3cb6b02c1..da77e2428 100644
--- a/src/nix-env/main.cc
+++ b/src/nix-env/main.cc
@@ -573,7 +573,7 @@ static void opQuery(Globals & globals,
         Strings columns;
         
         if (printStatus) {
-            Substitutes subs = querySubstitutes(i->drvPath);
+            Substitutes subs = querySubstitutes(noTxn, i->drvPath);
             columns.push_back(
                 (string) (installedPaths.find(i->outPath)
                     != installedPaths.end() ? "I" : "-")
diff --git a/src/nix-env/profiles.cc b/src/nix-env/profiles.cc
index 96467831f..abfdf9fed 100644
--- a/src/nix-env/profiles.cc
+++ b/src/nix-env/profiles.cc
@@ -62,11 +62,11 @@ Generations findGenerations(Path profile, int & curGen)
 
 
 static void makeNames(const Path & profile, unsigned int num,
-    Path & generation, Path & gcrootDrv)
+    Path & outLink, Path & drvLink)
 {
     Path prefix = (format("%1%-%2%") % profile % num).str();
-    generation = prefix + "-link";
-    gcrootDrv = prefix + "-drv.gcroot";
+    outLink = prefix + "-output";
+    drvLink = prefix + "-drv";
 }
 
 
@@ -79,20 +79,21 @@ Path createGeneration(Path profile, Path outPath, Path drvPath)
     unsigned int num = gens.size() > 0 ? gens.front().number : 0;
         
     /* Create the new generation. */
-    Path generation, gcrootDrv;
+    Path outLink, drvLink;
 
     while (1) {
-        makeNames(profile, num, generation, gcrootDrv);
-        if (symlink(outPath.c_str(), generation.c_str()) == 0) break;
+        makeNames(profile, num, outLink, drvLink);
+        if (symlink(outPath.c_str(), outLink.c_str()) == 0) break;
         if (errno != EEXIST)
-            throw SysError(format("creating symlink `%1%'") % generation);
+            throw SysError(format("creating symlink `%1%'") % outLink);
         /* Somebody beat us to it, retry with a higher number. */
         num++;
     }
 
-    writeStringToFile(gcrootDrv, drvPath);
+    if (symlink(drvPath.c_str(), drvLink.c_str()) != 0)
+        throw SysError(format("creating symlink `%1%'") % drvLink);
 
-    return generation;
+    return outLink;
 }
 
 
diff --git a/src/nix-store/main.cc b/src/nix-store/main.cc
index ea8d398f1..810fe94b6 100644
--- a/src/nix-store/main.cc
+++ b/src/nix-store/main.cc
@@ -274,61 +274,32 @@ static void opIsValid(Strings opFlags, Strings opArgs)
 
 static void opGC(Strings opFlags, Strings opArgs)
 {
-#if 0
+    GCAction action;
+    
     /* Do what? */
-    enum { soPrintLive, soPrintDead, soDelete } subOp;
-    time_t minAge = 0;
     for (Strings::iterator i = opFlags.begin();
          i != opFlags.end(); ++i)
-        if (*i == "--print-live") subOp = soPrintLive;
-        else if (*i == "--print-dead") subOp = soPrintDead;
-        else if (*i == "--delete") subOp = soDelete;
-        else if (*i == "--min-age") {
-            int n;
-            if (opArgs.size() == 0 || !string2Int(opArgs.front(), n))
-                throw UsageError("`--min-age' requires an integer argument");
-            minAge = n;
-        }
+        if (*i == "--print-live") action = gcReturnLive;
+        else if (*i == "--print-dead") action = gcReturnDead;
+        else if (*i == "--delete") action = gcDeleteDead;
         else throw UsageError(format("bad sub-operation `%1%' in GC") % *i);
-        
-    Paths roots;
+
+    /* Read the roots. */
+    PathSet roots;
     while (1) {
         Path root;
         getline(cin, root);
         if (cin.eof()) break;
-        roots.push_back(root);
+        roots.insert(root);
     }
 
-    PathSet live = findLivePaths(roots);
+    PathSet result;
+    collectGarbage(roots, action, result);
 
-    if (subOp == soPrintLive) {
-        for (PathSet::iterator i = live.begin(); i != live.end(); ++i)
+    if (action != gcDeleteDead) {
+        for (PathSet::iterator i = result.begin(); i != result.end(); ++i)
             cout << *i << endl;
-        return;
     }
-
-    PathSet dead = findDeadPaths(live, minAge * 3600);
-
-    if (subOp == soPrintDead) {
-        for (PathSet::iterator i = dead.begin(); i != dead.end(); ++i)
-            cout << *i << endl;
-        return;
-    }
-
-    if (subOp == soDelete) {
-
-        /* !!! What happens if the garbage collector run is aborted
-           halfway through?  In particular, dead paths can always
-           become live again (through re-instantiation), and might
-           then refer to deleted paths. => check instantiation
-           invariants */
-
-        for (PathSet::iterator i = dead.begin(); i != dead.end(); ++i) {
-            printMsg(lvlInfo, format("deleting `%1%'") % *i);
-            deleteFromStore(*i);
-        }
-    }
-#endif
 }