gnu: Put autoconf-related phases immediately after the 'unpack phase.

* gnu/packages/audio.scm (audacity, rtmidi)[arguments]: Correct phases
accordingly.
* gnu/packages/bioinformatics.scm (mash, seek, vsearch, emboss,
htslib-for-sambamba)[arguments]: Likewise.
* gnu/packages/ci.scm (cuirass)[arguments]: Likewise.
* gnu/packages/compression.scm (minizip, xdelta)[arguments]: Likewise.
* gnu/packages/cpp.scm (libzen)[arguments]: Likewise.
* gnu/packages/crypto.scm (opendht)[arguments]: Likewise.
* gnu/packages/databases.scm (4store, mdbtools)[arguments]: Likewise.
* gnu/packages/debug.scm (stress-make)[arguments]: Likewise.
* gnu/packages/dns.scm (dnscrypt-proxy, dnscrypt-wrapper)[arguments]:
Likewise.
* gnu/packages/emacs.scm (emacs-pdf-tools)[arguments]: Likewise.
* gnu/packages/embedded.scm (libjaylink, openocd)[arguments]: Likewise.
* gnu/packages/engineering.scm (gerbv)[arguments]: Likewise.
* gnu/packages/erlang.scm (erlang)[arguments]: Likewise.
* gnu/packages/ftp.scm (weex)[arguments]: Likewise.
* gnu/packages/gnome.scm (dia)[arguments]: Likewise.
* gnu/packages/gnunet.scm (gnurl, guile-gnunet)[arguments]: Likewise.
* gnu/packages/gtk.scm (guile-rsvg, graphene)[arguments]: Likewise.
* gnu/packages/guile.scm (guildhall, guile-ics, guile-sqlite3)[arguments]:
Likewise.
* gnu/packages/ibus.scm (ibus-libpinyin)[arguments]: Likewise.
* gnu/packages/irc.scm (weechat)[arguments]: Likewise.
* gnu/packages/java.scm (classpath-devel)[arguments]: Likewise.
* gnu/packages/libreoffice.scm (libetonyek)[arguments]: Likewise.
* gnu/packages/libusb.scm (hidapi)[arguments]: Likewise.
* gnu/packages/linux.scm (gpm)[arguments]: Likewise.
* gnu/packages/logging.scm (glog)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (ghmm)[arguments]: Likewise.
* gnu/packages/mail.scm (dovecot-trees, dovecot-libsodium-plugin, esmtp)
[arguments]: Likewise.
* gnu/packages/messaging.scm (freetalk, libmesode, libstrophe)[arguments]:
Likewise.
* gnu/packages/microcom.scm (microcom)[arguments]: Likewise.
* gnu/packages/ocaml.scm (ocaml-ssl)[arguments]: Likewise.
* gnu/packages/parallel.scm (slurm)[arguments]: Likewise.
* gnu/packages/pdf.scm (libharu)[arguments]: Likewise.
* gnu/packages/samba.scm (cifs-utils)[arguments]: Likewise.
* gnu/packages/serialization.scm (msgpack)[arguments]: Likewise.
* gnu/packages/shells.scm (scsh)[arguments]: Likewise.
* gnu/packages/telephony.scm (libiax2)[arguments]: Likewise.
* gnu/packages/textutils.scm (dotconf)[arguments]: Likewise.
* gnu/packages/version-control.scm (findnewest)[arguments]: Likewise.
* gnu/packages/video.scm (libmediainfo, mediainfo)[arguments]: Likewise.

39 files changed, 85 insertions, 86 deletions

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 16bca3b6b3..e27c13bed4 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -328,7 +328,7 @@ engineers, musicians, soundtrack editors and composers.")
        #:phases
        (modify-phases %standard-phases
          ;; FFmpeg is only detected if autoreconf runs.
-         (add-before 'configure 'autoreconf
+         (add-after 'unpack 'autoreconf
            (lambda _
              (zero? (system* "autoreconf" "-vfi")))))
        ;; The test suite is not "well exercised" according to the developers,
@@ -1979,8 +1979,8 @@ tempo and pitch of an audio recording independently of one another.")
     (arguments
      `(#:tests? #f ;no "check" target
        #:phases (modify-phases %standard-phases
-                  (add-before
-                   'configure 'autoconf
+                  (add-after
+                   'unpack 'autoconf
                    (lambda _ (zero? (system* "autoreconf" "-vfi"))))
                   (add-before
                    'build 'fix-makefile
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1f1b686c71..5e8eef4e1c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3450,7 +3450,7 @@ sequences).")
                (("^#include \"kseq\\.h\"")
                 "#include \"htslib/kseq.h\""))
              #t))
-         (add-before 'configure 'autoconf
+         (add-after 'fix-includes 'autoconf
            (lambda _ (zero? (system* "autoconf")))))))
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -4486,7 +4486,7 @@ distribution, coverage uniformity, strand specificity, etc.")
                        "Data2DB"
                        "PCL2Bin")))
            (modify-phases %standard-phases
-             (add-before 'configure 'bootstrap
+             (add-after 'unpack 'bootstrap
                (lambda _
                  (zero? (system* "bash" "gen_auto"))))
              (add-after 'build 'build-additional-tools
@@ -6164,8 +6164,8 @@ track.  The database is exposed as a @code{TxDb} object.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'autogen
-                     (lambda _ (zero? (system* "autoreconf" "-vif")))))))
+         (add-after 'unpack 'autogen
+           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
     (inputs
      `(("zlib" ,zlib)
        ("bzip2" ,bzip2)
@@ -8381,14 +8381,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
 AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available])
 AM_CONDITIONAL(AMPNG, true)"))
              #t))
-         (add-after 'unpack 'disable-update-check
+         (add-after 'fix-checks 'disable-update-check
            (lambda _
              ;; At build time there is no connection to the Internet, so
              ;; looking for updates will not work.
              (substitute* "Makefile.am"
                (("\\$\\(bindir\\)/embossupdate") ""))
              #t))
-         (add-before 'configure 'autogen
+         (add-after 'disable-update-check 'autogen
            (lambda _ (zero? (system* "autoreconf" "-vif")))))))
     (inputs
      `(("perl" ,perl)
@@ -9453,7 +9453,7 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
        (substitute-keyword-arguments (package-arguments htslib)
          ((#:phases phases)
           `(modify-phases  ,phases
-             (add-before 'configure 'bootstrap
+             (add-after 'unpack 'bootstrap
                (lambda _
                  (zero? (system* "autoreconf" "-vif"))))))))
       (native-inputs
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index d936c8fa10..c449754be8 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -216,7 +216,7 @@ their dependencies.")
                (substitute* "Makefile.am"
                  (("tests/repo.scm \\\\") "\\"))
                #t))
-           (add-before 'configure 'bootstrap
+           (add-after 'disable-repo-tests 'bootstrap
              (lambda _ (zero? (system* "sh" "bootstrap"))))
            (add-after 'install 'wrap-program
              (lambda* (#:key inputs outputs #:allow-other-keys)
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index bc10536766..a6758e9471 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -114,7 +114,7 @@ in compression.")
        (modify-phases %standard-phases
          (add-after 'unpack 'enter-source
            (lambda _ (chdir "contrib/minizip") #t))
-         (add-before 'configure 'autoreconf
+         (add-after 'enter-source 'autoreconf
            (lambda _
              (zero? (system* "autoreconf" "-vif")))))))
     (native-inputs
@@ -976,7 +976,7 @@ respectively, based on the reference implementation from Google.")
        (modify-phases %standard-phases
          (add-after 'unpack 'enter-build-directory
            (lambda _ (chdir "xdelta3")))
-         (add-before 'configure 'autoconf
+         (add-after 'enter-build-directory 'autoconf
            (lambda _ (zero? (system* "autoreconf" "-vfi")))))))
     (home-page "http://xdelta.com")
     (synopsis "Delta encoder for binary files")
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index da192553a5..5ad9fd33bc 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -45,12 +45,12 @@
      '(#:phases
        ;; build scripts not in root of archive
        (modify-phases %standard-phases
-         (add-before 'configure 'pre-configure
+         (add-after 'unpack 'pre-configure
            (lambda _
              (chdir "Project/GNU/Library")))
-         (add-before 'configure 'autogen
+         (add-after 'pre-configure 'autogen
            (lambda _
-             (zero? (system* "./autogen.sh")))))))
+             (zero? (system* "sh" "autogen.sh")))))))
     (home-page "https://github.com/MediaArea/ZenLib")
     (synopsis "C++ utility library")
     (description "ZenLib is a C++ utility library.  It includes classes for handling
diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index 0a05a10698..1783ae0945 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -161,7 +161,7 @@ OpenBSD tool of the same name.")
     (arguments
      `(#:configure-flags '("--disable-tools" "--disable-python")
        #:phases (modify-phases %standard-phases
-                  (add-before 'configure 'autoconf
+                  (add-after 'unpack 'autoconf
                     (lambda _
                       (zero? (system* "autoreconf" "-vfi")))))))
     (home-page "https://github.com/savoirfairelinux/opendht/")
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 93d59837bb..c6a9ff5bd6 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -115,9 +115,9 @@
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'generate-configure
+         (add-after 'unpack 'generate-configure
            (lambda _
-             (zero? (system* "./autogen.sh")))))))
+             (zero? (system* "sh" "autogen.sh")))))))
     ;; http://www.4store.org has been down for a while now.
     (home-page "https://github.com/garlik/4store")
     (synopsis "Clustered RDF storage and query engine")
@@ -1563,7 +1563,7 @@ for ODBC.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'autoreconf
+         (add-after 'unpack 'autoreconf
            (lambda _
              (zero? (system* "autoreconf" "-vfi")))))))
     (home-page "http://mdbtools.sourceforge.net/")
diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm
index 0fc1f513ba..43bfd9e514 100644
--- a/gnu/packages/debug.scm
+++ b/gnu/packages/debug.scm
@@ -319,7 +319,7 @@ down the road.")
              (add-before 'configure 'repack-make
                (lambda _
                  (zero? (system* "tar" "cJf" "./make.tar.xz" ,make-dir))))
-             (add-before 'configure 'bootstrap
+             (add-after 'unpack 'bootstrap
                (lambda _
                  (zero? (system* "autoreconf" "-vfi"))))))))
       (home-page "https://github.com/losalamos/stress-make")
diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm
index 702ed011f4..1716ca748c 100644
--- a/gnu/packages/dns.scm
+++ b/gnu/packages/dns.scm
@@ -181,7 +181,7 @@ high-volume and high-reliability applications. The name BIND stands for
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'autoreconf
+         (add-after 'unpack 'autoreconf
            (lambda _
              ;; Re-generate build files due to unbundling ltdl.
              ;; TODO: Prevent generating new libltdl and building it.
@@ -229,7 +229,7 @@ servers is included, and an up-to-date version is available at
        #:tests? #f
        #:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'create-configure
+         (add-after 'unpack 'create-configure
            (lambda _
              (zero? (system* "make" "configure")))))))
     (native-inputs
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 8955313e59..b3d5fc97e2 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -1273,7 +1273,7 @@ single buffer.")
          ;; Build server side using 'gnu-build-system'.
          (add-after 'unpack 'enter-server-dir
            (lambda _ (chdir "server") #t))
-         (add-before 'configure 'autogen
+         (add-after 'enter-server-dir 'autogen
            (lambda _
              (zero? (system* "bash" "autogen.sh"))))
 
diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm
index 5e51fe2d01..2a298dca9d 100644
--- a/gnu/packages/embedded.scm
+++ b/gnu/packages/embedded.scm
@@ -316,7 +316,7 @@ languages are C and C++.")
       (arguments
        `(#:phases
          (modify-phases %standard-phases
-           (add-before 'configure 'autoreconf
+           (add-after 'unpack 'autoreconf
              (lambda _
                (zero? (system* "autoreconf" "-vfi")))))))
       (home-page "http://repo.or.cz/w/libjaylink.git")
@@ -400,7 +400,7 @@ language.")
                         "presto" "openjtag")))
          #:phases
          (modify-phases %standard-phases
-           (add-before 'configure 'autoreconf
+           (add-after 'unpack 'autoreconf
              (lambda _
                (zero? (system* "autoreconf" "-vfi")))))))
       (home-page "http://openocd.org")
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index c4afe5ff95..0955bb4ae3 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -485,16 +485,16 @@ ready for production.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'autoconf
-          (lambda _
-            ;; Build rules contain references to Russian translation, but the
-            ;; needed files are missing; see
-            ;; http://sourceforge.net/p/gerbv/bugs/174/
-            (delete-file "po/LINGUAS")
-            (substitute* "man/Makefile.am"
-              (("PO_FILES= gerbv.ru.1.in.po") "")
-              (("man_MANS = gerbv.1 gerbv.ru.1") "man_MANS = gerbv.1"))
-            (zero? (system* "autoreconf" "-vfi")))))))
+         (add-after 'unpack 'autoconf
+           (lambda _
+             ;; Build rules contain references to Russian translation, but the
+             ;; needed files are missing; see
+             ;; http://sourceforge.net/p/gerbv/bugs/174/
+             (delete-file "po/LINGUAS")
+             (substitute* "man/Makefile.am"
+               (("PO_FILES= gerbv.ru.1.in.po") "")
+               (("man_MANS = gerbv.1 gerbv.ru.1") "man_MANS = gerbv.1"))
+             (zero? (system* "autoreconf" "-vfi")))))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
diff --git a/gnu/packages/erlang.scm b/gnu/packages/erlang.scm
index a400e712d5..cf4d7a5955 100644
--- a/gnu/packages/erlang.scm
+++ b/gnu/packages/erlang.scm
@@ -143,7 +143,7 @@
          (add-before 'configure 'set-erl-top
            (lambda _
              (setenv "ERL_TOP" (getcwd))))
-         (add-before 'configure 'autoconf
+         (add-after 'patch-source-env 'autoconf
            (lambda _ (zero? (system* "./otp_build" "autoconf"))))
          (add-after 'install 'patch-erl
            ;; This only works after install.
diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm
index bbdb4e410b..63a4054617 100644
--- a/gnu/packages/ftp.scm
+++ b/gnu/packages/ftp.scm
@@ -159,7 +159,7 @@ FTP browser, as well as non-interactive commands such as 'ncftpput' and
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'bootstrap
+         (add-after 'unpack 'bootstrap
            (lambda _ (zero? (system* "autoreconf" "-vfi")))))))
     (home-page "http://weex.sourceforge.net/")
     (synopsis "Non-interactive client for FTP synchronization")
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 43547961bf..5c94ceb036 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -312,7 +312,7 @@ either on a local, or remote machine via a number of methods.")
       (arguments
        `(#:phases
          (modify-phases %standard-phases
-           (add-before 'configure 'run-autogen
+           (add-after 'unpack 'run-autogen
              (lambda _
                (system* "sh" "autogen.sh"))))))
       (home-page "https://wiki.gnome.org/Apps/Dia")
diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm
index 837f9a21b6..426d0eec49 100644
--- a/gnu/packages/gnunet.scm
+++ b/gnu/packages/gnunet.scm
@@ -234,10 +234,10 @@ and support for SSL3 and TLS.")
               (rename-file (string-append out "/share/man/man3")
                            (string-append doc "/share/man/man3"))
               #t)))
-        (add-before 'configure 'autoconf
+        (add-after 'unpack 'autoconf
           ;; Clear artifacts left (shebangs) from release preparation.
           (lambda _
-            (zero? (system* "./buildconf"))))
+            (zero? (system* "sh" "buildconf"))))
         (replace 'check
           (lambda _
             ;; It is unclear why test1026 fails, however the content of it
@@ -345,7 +345,7 @@ kinds of basic applications for the foundation of a GNU internet.")
       (build-system gnu-build-system)
       (arguments
        '(#:phases (modify-phases %standard-phases
-                    (add-before 'configure 'bootstrap
+                    (add-after 'unpack 'bootstrap
                       (lambda _
                         (zero? (system* "autoreconf" "-vfi")))))))
       (native-inputs `(("pkg-config" ,pkg-config)
diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index 74f7b70ffe..1ea051bfb0 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -838,7 +838,7 @@ exceptions, macros, and a dynamic programming environment.")
       (build-system gnu-build-system)
       (arguments
        `(#:phases (modify-phases %standard-phases
-                    (add-before 'configure 'bootstrap
+                    (add-after 'unpack 'bootstrap
                       (lambda _
                         (zero? (system* "autoreconf" "-vfi")))))))
       (native-inputs `(("pkg-config" ,pkg-config)
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 6dacc472a8..0bcc524ed7 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -365,7 +365,7 @@ AM_SCM_LOG_FLAGS =  --no-auto-compile -s")
                  ;; reasons.  It does not fail when run outside of Guix.
                  (("tests/database.scm") ""))
                #t))
-           (add-before 'configure 'autogen
+           (add-after 'fix-bug-22 'autogen
              (lambda _
                (zero? (system* "sh" "autogen.sh")))))))
       (inputs
@@ -654,12 +654,12 @@ format is also supported.")
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases
-                  (add-before 'configure 'autoreconf
-                              (lambda _
-                                ;; Repository comes with a broken symlink
-                                (delete-file "README")
-                                (symlink "README.org" "README")
-                                (zero? (system* "autoreconf" "-fi")))))))
+                  (add-after 'unpack 'autoreconf
+                    (lambda _
+                      ;; Repository comes with a broken symlink
+                      (delete-file "README")
+                      (symlink "README.org" "README")
+                      (zero? (system* "autoreconf" "-fi")))))))
     (native-inputs
      `(("autoconf" ,(autoconf-wrapper))
        ("automake" ,automake)
@@ -1126,7 +1126,7 @@ Guile's foreign function interface.")
          ("sqlite" ,sqlite)))
       (arguments
        '(#:phases (modify-phases %standard-phases
-                    (add-before 'configure 'autoreconf
+                    (add-after 'unpack 'autoreconf
                       (lambda _
                         (zero? (system* "autoreconf" "-vfi"))))
                     (add-before 'build 'set-sqlite3-file-name
diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm
index 2200b6663d..7bbf2d6d7d 100644
--- a/gnu/packages/ibus.scm
+++ b/gnu/packages/ibus.scm
@@ -148,9 +148,9 @@ may also simplify input method development.")
    (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'autogen
-          (lambda _ (and (zero? (system* "intltoolize"))
-                         (zero? (system* "autoreconf" "-vif")))))
+         (add-after 'unpack 'autogen
+           (lambda _ (and (zero? (system* "intltoolize"))
+                          (zero? (system* "autoreconf" "-vif")))))
          (add-after 'wrap-program 'wrap-with-additional-paths
           (lambda* (#:key inputs outputs #:allow-other-keys)
             ;; Make sure 'ibus-setup-libpinyin' runs with the correct
diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm
index 0f68cc532a..2e8d3d4573 100644
--- a/gnu/packages/irc.scm
+++ b/gnu/packages/irc.scm
@@ -180,9 +180,9 @@ SILC and ICB protocols via plugins.")
                                 "--with-tclconfig="
                                 (assoc-ref %build-inputs "tcl") "/lib"))
        #:phases (modify-phases %standard-phases
-                  (add-before 'configure 'autogen
+                  (add-after 'unpack 'autogen
                     (lambda _
-                      (zero? (system* "./autogen.sh"))))
+                      (zero? (system* "sh" "autogen.sh"))))
                   (add-after 'install 'wrap
                     (lambda* (#:key inputs outputs #:allow-other-keys)
                       (let ((out (assoc-ref outputs "out"))
diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index fe43d01332..028fe06631 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -685,7 +685,7 @@ the standard javac executable.  The tool runs on JamVM instead of SableVM.")))
                "--disable-gjdoc")
          #:phases
          (modify-phases %standard-phases
-           (add-before 'configure 'bootstrap
+           (add-after 'remove-unsupported-anootations 'bootstrap
              (lambda _
                (zero? (system* "autoreconf" "-vif"))))
            (add-after 'unpack 'remove-unsupported-annotations
diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm
index cca222b1f8..d1e2e2e6e3 100644
--- a/gnu/packages/libreoffice.scm
+++ b/gnu/packages/libreoffice.scm
@@ -364,8 +364,8 @@ CorelDRAW documents of all versions.")
     (arguments
      `(#:configure-flags '("--with-mdds=1.2")
        #:phases (modify-phases %standard-phases
-                  (add-before 'configure 'autoreconf
-                              (lambda _ (system* "autoreconf"))))))
+                  (add-after 'unpack 'autoreconf
+                    (lambda _ (system* "autoreconf"))))))
     (native-inputs
      `(("cppunit" ,cppunit)
        ("doxygen" ,doxygen)
diff --git a/gnu/packages/libusb.scm b/gnu/packages/libusb.scm
index ed97ed9de7..f1d75220a9 100644
--- a/gnu/packages/libusb.scm
+++ b/gnu/packages/libusb.scm
@@ -332,7 +332,7 @@ devices.")
     (arguments
      '(#:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'bootstrap
+         (add-after 'unpack 'bootstrap
            (lambda _
              (zero? (system* "autoreconf" "-vfi")))))))
     (inputs
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 714c631fb1..dfb3dec2b9 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -3122,7 +3122,7 @@ write access to exFAT devices.")
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases
-                  (add-before 'configure 'bootstrap
+                  (add-after 'unpack 'bootstrap
                     (lambda _
                       ;; The tarball was not generated with 'make dist' so we
                       ;; need to bootstrap things ourselves.
diff --git a/gnu/packages/logging.scm b/gnu/packages/logging.scm
index b4f7caf56a..648a07e4c4 100644
--- a/gnu/packages/logging.scm
+++ b/gnu/packages/logging.scm
@@ -75,7 +75,7 @@ staying as close to their API as is reasonable.")
        ("libtool" ,libtool)))
     (arguments
      '(#:phases (modify-phases %standard-phases
-                  (add-before 'configure 'add-automake-files
+                  (add-after 'unpack 'add-automake-files
                     (lambda _
                       ;; The 'test-driver' file is a dangling symlink to
                       ;; /usr/share/automake; replace it.  We can't just run
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index c5132faf58..58b47dacd1 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -190,9 +190,9 @@ classification.")
                                  "@unittest.skip(\"Disabled by Guix\")\n"
                                  line)))
                #t))
-           (add-before 'configure 'autogen
+           (add-after 'disable-broken-tests 'autogen
              (lambda _
-               (zero? (system* "bash" "./autogen.sh")))))))
+               (zero? (system* "bash" "autogen.sh")))))))
       (inputs
        `(("python" ,python-2) ; only Python 2 is supported
          ("libxml2" ,libxml2)))
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index fe040a1180..2a759c3d2e 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -1169,9 +1169,9 @@ It supports mbox/Maildir and its own dbox/mdbox formats.")
                                               "/lib/dovecot"))
        #:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'autogen
+         (add-after 'unpack 'autogen
            (lambda _
-             (zero? (system* "./autogen.sh")))))))
+             (zero? (system* "sh" "autogen.sh")))))))
     (home-page "https://0xacab.org/riseuplabs/trees")
     (synopsis "NaCL-based Dovecot email storage encryption plugin")
     (description
@@ -1225,9 +1225,9 @@ using lidsodium sealed boxes.
                                                 "/lib/dovecot"))
          #:phases
          (modify-phases %standard-phases
-           (add-before 'configure 'autogen
+           (add-after 'unpack 'autogen
              (lambda _
-               (zero? (system* "./autogen.sh")))))))
+               (zero? (system* "sh" "autogen.sh")))))))
       (home-page "https://github.com/LuckyFellow/dovecot-libsodium-plugin")
       (synopsis "Libsodium password hashing schemes plugin for Dovecot")
       (description
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index c69bd8b101..52ca4bef79 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -1209,7 +1209,7 @@ support, and more.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'autogen
+         (add-after 'unpack 'autogen
            (lambda _
              (zero? (system* "sh" "autogen.sh"))))
          ;; For 'system' commands in Scheme code.
diff --git a/gnu/packages/microcom.scm b/gnu/packages/microcom.scm
index aa42e99213..dcb864808f 100644
--- a/gnu/packages/microcom.scm
+++ b/gnu/packages/microcom.scm
@@ -42,7 +42,7 @@
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'bootstrap
+         (add-after 'unpack 'bootstrap
            (lambda _
              (zero? (system* "autoreconf" "-i")))))))
     (inputs `(("readline" ,readline)))
diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 2597775bf7..700c5698ed 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -1631,9 +1631,9 @@ lets the client choose the concrete timeline.")
                  #:make-flags (list "OCAMLFIND_LDCONF=ignore")
                  #:phases
                  (modify-phases %standard-phases
-                   (add-before 'configure 'bootstrap
+                   (add-after 'unpack 'bootstrap
                      (lambda* (#:key #:allow-other-keys)
-                       (system* "./bootstrap")
+                       (system* "sh" "bootstrap")
                        (substitute* "src/OCamlMakefile"
                          (("/bin/sh") (which "bash")))
                        (substitute* "configure"
diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index db04a5704e..5101838d26 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -136,9 +136,8 @@ and they are executed on lists of files, hosts, users or other items.")
             (string-append "--with-ssl=" (assoc-ref %build-inputs "openssl")))
       #:phases
       (modify-phases %standard-phases
-       (add-before
-        'configure 'autogen
-        (lambda _ (zero? (system* "autoconf"))))))) ; configure.ac was patched
+        (add-after 'unpack 'autogen
+          (lambda _ (zero? (system* "autoconf"))))))) ; configure.ac was patched
    (home-page "http://slurm.schedmd.com/")
    (synopsis "Workload manager for cluster computing")
    (description
diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index 0993543c20..5e52d87ca5 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -254,7 +254,7 @@ Poppler PDF rendering library.")
                            (assoc-ref %build-inputs "libpng")))
       #:phases
       (modify-phases %standard-phases
-        (add-before 'configure 'autogen
+        (add-after 'unpack 'autogen
           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
    (inputs
     `(("zlib" ,zlib)
diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm
index 116d7f60ec..1fc4994ab3 100644
--- a/gnu/packages/samba.scm
+++ b/gnu/packages/samba.scm
@@ -71,7 +71,7 @@
      `(#:phases
        (modify-phases %standard-phases
          ;; The 6.7 tarball is missing ‘install.sh’. Create it.
-         (add-before 'configure 'autoreconf
+         (add-after 'unpack 'autoreconf
            (lambda _
              (zero? (system* "autoreconf" "-i"))))
          (add-before 'configure 'set-root-sbin
diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 54ccbf7c79..1866926129 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -127,7 +127,7 @@ such as compact binary encodings, XML, or JSON.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'autoconf
+         (add-after 'unpack 'autoconf
            (lambda _
              (system* "autoreconf" "-vfi"))))))
     (home-page "http://www.msgpack.org")
diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm
index 09a6c3a03f..f03d7c4a9d 100644
--- a/gnu/packages/shells.scm
+++ b/gnu/packages/shells.scm
@@ -430,7 +430,7 @@ use of experts and novices alike.")
                  (delete-file-recursively "rx")
                  (symlink rxpath "rx"))
                #t))
-           (add-before 'configure 'autoreconf
+           (add-after 'unpack 'autoreconf
              (lambda _
                (zero? (system* "autoreconf")))))))
       (inputs
diff --git a/gnu/packages/telephony.scm b/gnu/packages/telephony.scm
index c3bf203602..5751015260 100644
--- a/gnu/packages/telephony.scm
+++ b/gnu/packages/telephony.scm
@@ -272,7 +272,7 @@ and a supporting cryptographic kernel.")
          ("libtool" ,libtool)))
       (arguments
        `(#:phases (modify-phases %standard-phases
-                    (add-before 'configure 'autoconf
+                    (add-after 'unpack 'autoconf
                       (lambda _
                         (zero? (system* "autoreconf" "-vfi")))))))
       (home-page "https://gitlab.savoirfairelinux.com/sflphone/libiax2")
diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 70b057ffd3..3359ab4845 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -579,7 +579,7 @@ categories.")
      `(#:tests? #f ; FIXME maketest.sh does not work.
        #:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'autoreconf
+         (add-after 'unpack 'autoreconf
            (lambda _
              (zero? (system* "autoreconf" "-vif")))))))
     (native-inputs
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 36a6b7cd18..0657df67a1 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -1263,7 +1263,7 @@ output of the 'git' command.")
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases
-                  (add-before 'configure 'bootstrap
+                  (add-after 'unpack 'bootstrap
                     (lambda _
                       (zero? (system* "autoreconf" "-vfi")))))))
     (native-inputs `(("autoconf" ,autoconf)
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 4eb6b8b6e8..3924e93f96 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -2253,9 +2253,9 @@ practically any type of media.")
          (add-before 'configure 'pre-configure
            (lambda _
              (chdir "Project/GNU/Library")))
-         (add-before 'configure 'autogen
+         (add-after 'unpack 'autogen
            (lambda _
-             (zero? (system* "./autogen.sh")))))))
+             (zero? (system* "sh" "autogen.sh")))))))
     (home-page "https://mediaarea.net/en/MediaInfo")
     (synopsis "Library for retrieving media metadata")
     (description "MediaInfo is a library used for retrieving technical
@@ -2311,9 +2311,9 @@ MPEG-2, MPEG-4, DVD (VOB)...
          (add-before 'configure 'pre-configure
            (lambda _
              (chdir "Project/GNU/CLI")))
-         (add-before 'configure 'autogen
+         (add-after 'unpack 'autogen
            (lambda _
-             (zero? (system* "./autogen.sh")))))))
+             (zero? (system* "sh" "autogen.sh")))))))
     (home-page "https://mediaarea.net/en/MediaInfo")
     (synopsis "Utility for reading media metadata")
     (description "MediaInfo is a utility used for retrieving technical