diff --git a/pkgs/applications/science/math/maxima/default.nix b/pkgs/applications/science/math/maxima/default.nix
index 21d3c656d30..4981767f21f 100644
--- a/pkgs/applications/science/math/maxima/default.nix
+++ b/pkgs/applications/science/math/maxima/default.nix
@@ -1,8 +1,8 @@
-{ stdenv, fetchurl, sbcl, texinfo, perl, makeWrapper, rlwrap ? null, tk ? null, gnuplot ? null }:
+{ stdenv, fetchurl, sbcl, texinfo, perl, python, makeWrapper, rlwrap ? null, tk ? null, gnuplot ? null }:
 
 let
   name    = "maxima";
-  version = "5.36.1";
+  version = "5.38.1";
 
   searchPath =
     stdenv.lib.makeBinPath
@@ -13,10 +13,10 @@ stdenv.mkDerivation {
 
   src = fetchurl {
     url = "mirror://sourceforge/${name}/${name}-${version}.tar.gz";
-    sha256 = "0x1rk659sn3cq0n5c90848ilzr1gb1wf0072fl6jhkdq00qgh2s0";
+    sha256 = "1p6646rvq43hk09msyp0dk50cqpkh07mf4x0bc2fqisqmcv6b1hf";
   };
 
-  buildInputs = [sbcl texinfo perl makeWrapper];
+  buildInputs = [sbcl texinfo perl python makeWrapper];
 
   postInstall = ''
     # Make sure that maxima can find its runtime dependencies.
diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix
index 6e0b4313b47..9e17fe60c29 100644
--- a/pkgs/applications/science/math/sage/default.nix
+++ b/pkgs/applications/science/math/sage/default.nix
@@ -7,7 +7,7 @@ stdenv.mkDerivation rec {
   name = "sage-6.8";
 
   src = fetchurl {
-    url = "mirror://sagemath/${name}.tar.gz";
+    url = "http://old.files.sagemath.org/src-old/${name}.tar.gz";
     sha256 = "102mrzzi215g1xn5zgcv501x9sghwg758jagx2jixvg1rj2jijj9";
   };
 
@@ -18,11 +18,14 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
+  hardeningDisable = [ "format" ];
+
   preConfigure = ''
     export SAGE_NUM_THREADS=$NIX_BUILD_CORES
     export SAGE_ATLAS_ARCH=fast
     mkdir -p $out/sageHome
     export HOME=$out/sageHome
+    export CPPFLAGS="-P"
   '';
 
   preBuild = "patchShebangs build";
@@ -30,7 +33,6 @@ stdenv.mkDerivation rec {
   installPhase = ''DESTDIR=$out make install'';
 
   meta = {
-    broken = true;
     homepage = "http://www.sagemath.org";
     description = "A free open source mathematics software system";
     license = stdenv.lib.licenses.gpl2Plus;
diff --git a/pkgs/development/haskell-modules/configuration-common.nix b/pkgs/development/haskell-modules/configuration-common.nix
index b84307a9dbf..9fa66338d8c 100644
--- a/pkgs/development/haskell-modules/configuration-common.nix
+++ b/pkgs/development/haskell-modules/configuration-common.nix
@@ -998,4 +998,7 @@ self: super: {
     '';
   });
 
+  # https://bitbucket.org/ssaasen/spy/pull-requests/3/fsnotify-dropped-system-filepath
+  spy = appendPatch super.spy ./patches/spy.patch;
+
 }
diff --git a/pkgs/development/haskell-modules/generic-stack-builder.nix b/pkgs/development/haskell-modules/generic-stack-builder.nix
index 09bd38ccc93..c7cfbef7d13 100644
--- a/pkgs/development/haskell-modules/generic-stack-builder.nix
+++ b/pkgs/development/haskell-modules/generic-stack-builder.nix
@@ -19,12 +19,13 @@ stdenv.mkDerivation (args // {
   STACK_PLATFORM_VARIANT="nix";
   STACK_IN_NIX_SHELL=1;
   STACK_IN_NIX_EXTRA_ARGS =
-    concatMap (pkg: ["--extra-lib-dirs=${pkg}/lib"
-                     "--extra-include-dirs=${pkg}/include"]) buildInputs ++
+    concatMap (pkg: ["--extra-lib-dirs=${getLib pkg}/lib"
+                     "--extra-include-dirs=${getDev pkg}/include"]) buildInputs ++
     extraArgs;
 
   # XXX: workaround for https://ghc.haskell.org/trac/ghc/ticket/11042.
   LD_LIBRARY_PATH = makeLibraryPath (LD_LIBRARY_PATH ++ buildInputs);
+                    # ^^^ Internally uses `getOutput "lib"` (equiv. to getLib)
 
   preferLocalBuild = true;
 
diff --git a/pkgs/development/haskell-modules/patches/spy.patch b/pkgs/development/haskell-modules/patches/spy.patch
new file mode 100644
index 00000000000..4c4e1844361
--- /dev/null
+++ b/pkgs/development/haskell-modules/patches/spy.patch
@@ -0,0 +1,26 @@
+diff --git a/src/Spy/Watcher.hs b/src/Spy/Watcher.hs
+     index 8512613..4df67d4 100644
+--- a/src/Spy/Watcher.hs
++++ b/src/Spy/Watcher.hs
+@@ -50,7 +50,7 @@ plainFormat = Plain
+ spy :: Spy -> IO b -> IO ()
+ spy config after = withManager $ \wm ->
+     runIndefinitely
+-      (watchTree wm (decodeString $ dir config)
++      (watchTree wm (dir config)
+                   (not . skipEvent config . eventPath)
+                   (handleEvent config)) 
+       (const after)
+@@ -106,9 +106,9 @@ eventTime (Modified _ t) = t
+ eventTime (Removed _ t) = t
+ 
+ eventPath :: Event -> FilePath
+-eventPath (Added fp _) = encodeString fp
+-eventPath (Modified fp _) = encodeString fp
+-eventPath (Removed fp _) = encodeString fp
++eventPath (Added fp _) = fp
++eventPath (Modified fp _) = fp
++eventPath (Removed fp _) = fp
+ 
+ eventType :: Event -> FilePath
+ eventType (Added _ _) = "Added"
diff --git a/pkgs/development/tools/build-managers/bear/default.nix b/pkgs/development/tools/build-managers/bear/default.nix
new file mode 100644
index 00000000000..cc34a73ecd5
--- /dev/null
+++ b/pkgs/development/tools/build-managers/bear/default.nix
@@ -0,0 +1,32 @@
+{ stdenv, fetchFromGitHub, cmake, python }:
+
+stdenv.mkDerivation rec {
+  name = "bear-${version}";
+  version = "2.2.0";
+
+  src = fetchFromGitHub {
+    owner = "rizsotto";
+    repo = "Bear";
+    rev = version;
+    sha256 = "08llfqg8y6d7vfwaw5plrk1rrqzs0ywi2ldnlwvy917603971rg0";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ python ]; # just for shebang of bin/bear
+
+  doCheck = false; # all fail
+
+  meta = with stdenv.lib; {
+    description = "Tool that generates a compilation database for clang tooling";
+    longDescription = ''
+      Note: the bear command is very useful to generate compilation commands
+      e.g. for YouCompleteMe.  You just enter your development nix-shell
+      and run `bear make`.  It's not perfect, but it gets a long way.
+    '';
+    homepage = https://github.com/rizsotto/Bear;
+    license = licenses.gpl3Plus;
+    platforms = platforms.unix;
+    maintainers = [ maintainers.vcunat ];
+  };
+}
+
diff --git a/pkgs/development/tools/rtags/default.nix b/pkgs/development/tools/rtags/default.nix
index 06ab4ffed3c..959681c7e1a 100644
--- a/pkgs/development/tools/rtags/default.nix
+++ b/pkgs/development/tools/rtags/default.nix
@@ -2,8 +2,7 @@
 
 stdenv.mkDerivation rec {
   name = "rtags-${version}";
-  version = "git-2016-04-29";
-  rev = "233543d343bf86fa31c35ee21242fa2da3a965ab";
+  version = "2.3";
 
   buildInputs = [ cmake llvmPackages.llvm openssl llvmPackages.clang emacs ];
 
@@ -13,10 +12,10 @@ stdenv.mkDerivation rec {
   '';
 
   src = fetchgit {
-    inherit rev;
+    rev = "refs/tags/v${version}";
     fetchSubmodules = true;
     url = "https://github.com/andersbakken/rtags.git";
-    sha256 = "10j1s7kvnd5823p1kgx3hyca9jz9j27y6xk0q208p095wf8hk105";
+    sha256 = "05kzch88x2wiimygfli6vsr9i5hzgkybsya8qx4zvb6daip4b7yf";
   };
 
   meta = {
diff --git a/pkgs/misc/vim-plugins/default.nix b/pkgs/misc/vim-plugins/default.nix
index 6a49103a2f7..67ea56be847 100644
--- a/pkgs/misc/vim-plugins/default.nix
+++ b/pkgs/misc/vim-plugins/default.nix
@@ -13,7 +13,8 @@ in
 
 # TL;DR
 # Add your plugin to ./vim-plugin-names
-# Generate via `vim-plugin-names-to-nix`
+# Regenerate via `nix-build -Q -A vimPlugins.pluginnames2nix; ./result/bin/vim-plugin-names-to-nix`
+# Copy the generated expression(s) into this file.
 # If plugin is complicated then make changes to ./vim2nix/additional-nix-code
 
 # This attrs contains two sections:
@@ -885,6 +886,17 @@ rec {
 
   };
 
+  vim-indent-guides = buildVimPluginFrom2Nix { # created by nix#NixDerivation
+    name = "vim-indent-guides-2016-04-17";
+    src = fetchgit {
+      url = "git://github.com/nathanaelkane/vim-indent-guides";
+      rev = "018298ead9d3aa9cd3b4ae222f81022a33978b09";
+      sha256 = "0zyrs9r3vza2kqhqir6qpkygy6yljpn877bvycspv89ljzczmwrs";
+    };
+    dependencies = [];
+
+  };
+
   vim-stylish-haskell = buildVimPluginFrom2Nix { # created by nix#NixDerivation
     name = "vim-stylish-haskell-2015-05-10";
     src = fetchgit {
diff --git a/pkgs/misc/vim-plugins/vim-plugin-names b/pkgs/misc/vim-plugins/vim-plugin-names
index 8f09ea935ed..6cef8885ce0 100644
--- a/pkgs/misc/vim-plugins/vim-plugin-names
+++ b/pkgs/misc/vim-plugins/vim-plugin-names
@@ -68,6 +68,7 @@
 "github:mhinz/vim-startify"
 "github:mkasa/lushtags"
 "github:mpickering/hlint-refactor-vim"
+"github:nathanaelkane/vim-indent-guides"
 "github:nbouscal/vim-stylish-haskell"
 "github:neovimhaskell/haskell-vim"
 "github:osyo-manga/shabadou.vim"
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index afb1e6c6fc0..302069fd521 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -6145,6 +6145,8 @@ in
 
   bazel = callPackage ../development/tools/build-managers/bazel { jdk = openjdk8; };
 
+  bear = callPackage ../development/tools/build-managers/bear { };
+
   bin_replace_string = callPackage ../development/tools/misc/bin_replace_string { };
 
   binutils = if stdenv.isDarwin then self.darwin.binutils else self.binutils-raw;