[gentoo-commits] repo/gentoo:master commit in: sci-mathematics/isabelle/files/, sci-mathematics/isabelle/

[James Le Cuirot]

commit:     1db4669fbb720d89e5420eb5a5b1c7b0ca508aa6
Author:     James Le Cuirot <chewi <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  6 12:52:23 2016 +0000
Commit:     James Le Cuirot <chewi <AT> gentoo <DOT> org>
CommitDate: Sun Mar  6 13:01:33 2016 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1db4669f

sci-mathematics/isabelle: Remove old

Package-Manager: portage-2.2.27

 sci-mathematics/isabelle/Manifest                  |  10 -
 .../files/isabelle-2011.1-gentoo-settings.patch    |  39 ---
 .../files/isabelle-2011.1-graphbrowser.patch       |  11 -
 .../isabelle/files/isabelle-2011.1-libsha1.patch   |  11 -
 .../isabelle-2011.1-proofgeneral-gentoo-path.patch |  39 ---
 ...isabelle-2011.1-reverse-line-editor-order.patch |  12 -
 .../files/isabelle-2012-gentoo-settings.patch      |  62 ----
 ...t-equations-in-function-definitions-error.patch |  35 --
 .../files/isabelle-2012-signal-handling.patch      |   8 -
 ...belle-2013-HOL-Predicate_Compile_Examples.patch |  82 -----
 .../isabelle/files/isabelle-2013-classpath.patch   | 149 --------
 .../isabelle/files/isabelle-2013.2-classpath.patch | 135 --------
 sci-mathematics/isabelle/isabelle-2011.1-r2.ebuild | 254 --------------
 sci-mathematics/isabelle/isabelle-2011.1.ebuild    | 142 --------
 sci-mathematics/isabelle/isabelle-2012-r1.ebuild   | 320 ------------------
 sci-mathematics/isabelle/isabelle-2013-r2.ebuild   | 353 -------------------
 sci-mathematics/isabelle/isabelle-2013.2-r1.ebuild | 375 ---------------------
 sci-mathematics/isabelle/metadata.xml              |  15 -
 18 files changed, 2052 deletions(-)

diff --git a/sci-mathematics/isabelle/Manifest 
b/sci-mathematics/isabelle/Manifest
index 87a47c5..8e612b8 100644
--- a/sci-mathematics/isabelle/Manifest
+++ b/sci-mathematics/isabelle/Manifest
@@ -1,17 +1,7 @@
-DIST Isabelle2011-1.tar.gz 42239059 SHA256 
48d77fe31a16b44f6015aa7953a60bdad8fcec9e60847630dc7b98c053edfc08 SHA512 
213207951455395659a91b0bc6c8520c084cb6c75098c8f24c0800e41474c90c92aae86ffb99415142f6cf63d569556661ba350024fe458daa54a5cc9db372fd
 WHIRLPOOL 
7e7868c3f464f507aceb8e1f648c04394fdd69746242179e66cfad64f927cf4d6aba41970428da5e45cce90a30bcee29bdc373d8a9e4943eb61cd97480d0a366
-DIST Isabelle2012-doc-src.tar.gz 2688496 SHA256 
e18965fe0f7f89b286d4707e38201f1edbea81f6b26aed59d63a633c03fec097 SHA512 
5aaea56eb67e535d745d63314278b6ee8469e6d3bbf4ce4d7b3f5e04b24557783b56d50d905a5ad69187c42f44407023c95a9bfb6faab125c21edff7638ff21d
 WHIRLPOOL 
278b63a243950b1596376ee04cbfddb7a93c747e9f6ee66c5b069ca0dae4ca8d10bef43e03069b6186a19c703f71a585633fc47c3c1a15de3a886ff468232127
-DIST Isabelle2012.tar.gz 49529865 SHA256 
b86f957dee221041f92c9d4ced4758d45b4950339743d0d58b1ea6061e2b53f0 SHA512 
1346f563233eba10bc14f7d140706b8bfba8e832f7ee5887316c829926136af07d700914a925272d8adc1275b0bdd682540518957910c136a15bfc60d61285a0
 WHIRLPOOL 
23b764a1a0044a9525d058e95da318f4425fadf7660edc8ab8f35b248f98dcff0dba2e533ff18d8bf47ea164cec12a9648642749de2a49887bbe84ed4e71a68b
-DIST Isabelle2013-2.tar.gz 52603110 SHA256 
602e91377b0999c25950ae2a34c0fcb23e3aff3a196bdbc5ce61634bd90d7f22 SHA512 
464a2735b2f4e28dcf44e55cd4abb4d8766a6bb7eb86f989f3592e7819e33d97922bdfb6701da85aa9d7c4cc2aee3eadebde1c7e3fc74bb3f6108a5daf5fea45
 WHIRLPOOL 
0dc354d60e3440ea0909dc09f25b66cb301b82f88fbe21c0b7f4bfef40ecc3631014757abd8657f0464047f0ad32827ad308e3f998fcf2477e05907ff7b19a84
-DIST Isabelle2013.tar.gz 54638791 SHA256 
2f2cda9939248bd4346ad7e074cb6b2cfad70708777491c6262a5ae670c8f83a SHA512 
e03f9b747f678749a562c3de6100f4f4e010ace51b2eb13bcde0a63591eec0cb4e081f7fad9147d022fe787b56eac3f037ab3a296080fd70cc7d058ea961a789
 WHIRLPOOL 
5cbcbc93bd2ce4723034c3d95d4678b2de90c924601b795c5da378cb76f58275e5d5f47ce9120234a9ea36e43ab759ced843dca76942378abfa1fb7aff858a65
 DIST Isabelle2015.tar.gz 36529154 SHA256 
08723d3be6f91c57a7a69a8624c54cc1e0cd31506988bf29ed365a5aa5a5156f SHA512 
052bb80316a9345368a295a7c5f3869b58d71a6879548fc6240a04fd2cf8c11406274ead8a1ed098563ef9b7573a826656da543e745044fc1d275322af5cc212
 WHIRLPOOL 
0be4759a1064f4759c2f227b037c448093ff36b47e16002fbb7e99d2843583e01314c4ea5c7a8cbf4d1304f8f72a383052911e483d51e4af2e68c4c36dea5121
 DIST csdp-isabelle-component-6.x.tar.gz 493 SHA256 
65dde42fa476095052ca3820df4c0e45089653d4467a53de711c8e13670a1b19 SHA512 
9be28ecbf61d0f6ad23e28d44bd7ceb8f06ab22f3a05a7c823a9c5bf52ddcf5e5c300c41e14451d6b8e6a4c32b1bbd17769c731cd890fab335a866cd5e735290
 WHIRLPOOL 
c930c531637172e4c75ec44d68f71e69e748a8b976fa3651ef4015fb6a90e30b568bd092632dc16c6389aac09bc13f3249af6c3ac261f09ad2dc5ad915282f99
 DIST exec_process-isabelle-component-1.0.3.tar.gz 814 SHA256 
ee3b7b299852bcfd0bf7ffce6c8cd2279f2d71247c4a7b0042971b31c2b2a89d SHA512 
7880b7f9843ff5806ab37d938a817a5b33e973772d9a6c6cf76bf04076fb532309bd22dfaa203be7c72c07f5a638f0f97e730c414ed164024fd31f1f09fc7c09
 WHIRLPOOL 
9d9beb7a41baac8b591ceee31bb7b69e1dd07fce66757511649977f6a85d85eef525ba0be13b0873c1aef47de0eace8bf88283b4a136397000e61cfc81da8d4d
-DIST jedit_build-20120414.tar.gz 7509120 SHA256 
3c5840fd01b87013b05a92742d41f66f655df6fe9edef1525c6722f92d8f3e41 SHA512 
2e2f0db4964a041ba54382a9c787246e1d433e43167019c6ea8d4cf6beb84ce438c0bc559d2588229b0166c91bac603bed39abc45d5d4267020f55eaba1aaa0c
 WHIRLPOOL 
40b883943bde312b4c7adc43607ba4759e5ebe22cab3c922c81393375f917af21d4a8dc068e5692ffcf7bdfb1e7fe3081358dc8e346d1942582bf79e249b0cbb
-DIST jedit_build-isabelle-component-20130104.tar.gz 10734679 SHA256 
22a4880deb1054a548476b22662b42bfaf5394ceb07b30eba69be433bcea1074 SHA512 
bacdb3ca73d48fe9ba71dd32cd68e98333831f205dd3ced69bb9344c5b167ba084662f1108690f371b4b64f6b786955a332bcd51a2dc21c2179fb1b4727430dd
 WHIRLPOOL 
fc97923e08202e117ca3112b69f74a9f4663a70f55fa051ac55e02c85be57423f762263cac2ded33d9c2f412736e4fa0937aa07df3f36b915e806959055a796b
-DIST jedit_build-isabelle-component-20131106.tar.gz 8796625 SHA256 
a13a896263804f5aee82db0e1fe6be7982abe3ca1266cd15f7fe9c8c2f6e2ba5 SHA512 
7fc3313916cd408c906e453a4895f49223a8b9dc1e2c577c16468394b73a3724449b411521884d419683cd3d2eb3ef59929608483ff092b9b0e3663efd5e136e
 WHIRLPOOL 
4e7c933df7eea5b9c312f8e0c2c46d44a442d0dd2bb76415bea1fcf307ff75d1f8fb592fe4cad647674dc387fe6fa017dbf4e0cf2ec64459bdafb093470e2abf
 DIST jedit_build-isabelle-component-20150228.tar.gz 10674317 SHA256 
2bee3c5242a3ce4150656f106e658096e82b6bd966e04d590e20023a956be29b SHA512 
ba2d0804f21cee596fc3528a592941efc393e98b890efe054aed18fc0d31edfe459047b58ed79b42892e219b4c35a4fb5c8cca0f402b96d641ff8ce62e321339
 WHIRLPOOL 
b2971bdef70e32d858385cb58603d6a5a7e357dbbc9810569093a31332a7838387f43a76a65048a12f259f08de86f200e962ccf2deb2bd3cd4e83dc4c1e41d8b
 DIST jfreechart-isabelle-component-1.0.14-1.tar.gz 3444825 SHA256 
b0eb7365c4c5877379889100f081a4afc4117afc0d332941c3dd01bef2c4aee9 SHA512 
ee1d84a45e43029d5e3acee823176196da19789322e8d3c2c81d5504930ad81d50e16e5da87655e4151034901daefb4ce6b82334839e39134b3a7ce32203aa67
 WHIRLPOOL 
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-DIST jfreechart-isabelle-component-1.0.14.tar.gz 3443727 SHA256 
c873ad6f07edbcceb5c76aac2e848c7d7f12c78c93c05f7e97c4b1fdba7c2df0 SHA512 
c55ec01b215368f064de2f288f788960a256445adca5565c00aa9c0fab5732707a9e72bcdb3838676c80e735c520b9948855d7a32b9076bf35f1a279320ee72a
 WHIRLPOOL 
ba1a75e21525c302a3b755d814502dad60c540c2004dd894f60fdd6966766f85d71bbb45728ca220a4a7cff334de81db756fbb89e1059f32e248cabf0a7b97d6
-DIST polyml-isabelle-component-5.5.1-1.tar.gz 831 SHA256 
f19a4dfc3117792423270cb98a5c406f7339f4bd7715c16976a281d964792844 SHA512 
35ab69d0fd2737f3c6a13ca022103428bcb0e71032304d244614d271848b9ae8986da25bd4ef02668eef169f3a3a72576a619152ce3cbf036af7aa365e857c1a
 WHIRLPOOL 
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 DIST polyml-isabelle-component-5.5.2-3.tar.gz 691 SHA256 
1ba253974193efc70711b7fe32cc831d8bcc13107b0b130ddf6087bb6ff6d3e7 SHA512 
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 WHIRLPOOL 
3a85c59b1bb928c5ea91f8150c6ded5309fae96bd7558b56e6c3d8f04c418b03b57fb49565af5ed919179fd9e30c957575ca7b65d938ce69c5d3131d8c55ab1e
 DIST xz-java-isabelle-component-1.5.tar.gz 315 SHA256 
e7fdd433608561c87558d4d0ee39166e8396ce11242e85391417ec7fd3ce7b8e SHA512 
6dfec49e12c4cafbb6b6386dd54477e86b6bb419a77c52d9606a0305aeea9cd11f087ed6bba77352c7bf9ec656052ef617e845f472e57b5cdfbccf22b2eeb4fa
 WHIRLPOOL 
9c1fc16db0adc88557b81608902d9d69007dc90d5849f4f7501101930842ce81ded76af0e76e38df8bd0b07d137e53bafaa338bf6c7ae338e97af2a1433d5c1d

diff --git 
a/sci-mathematics/isabelle/files/isabelle-2011.1-gentoo-settings.patch 
b/sci-mathematics/isabelle/files/isabelle-2011.1-gentoo-settings.patch
deleted file mode 100644
index 67e3476..0000000
--- a/sci-mathematics/isabelle/files/isabelle-2011.1-gentoo-settings.patch
+++ /dev/null
@@ -1,39 +0,0 @@
---- Isabelle2011-1-orig/etc/settings   2011-10-10 01:47:58.000000000 +1100
-+++ Isabelle2011-1/etc/settings        2012-01-01 16:33:27.922565527 +1100
-@@ -24,9 +24,16 @@
-   "/usr/share/polyml/$ML_PLATFORM" \
-   "/opt/polyml/$ML_PLATFORM" \
-   "")"
--ML_SYSTEM=$("$ISABELLE_HOME/lib/scripts/polyml-version")
--ML_OPTIONS="-H 200"
--ML_SOURCES="$ML_HOME/../src"
-+# ML_SYSTEM=$("$ISABELLE_HOME/lib/scripts/polyml-version")
-+# ML_OPTIONS="-H 200"
-+# ML_SOURCES="$ML_HOME/../src"
-+
-+# Poly/ML 5.4.0 (64 bit)
-+ML_PLATFORM=x86_64-linux
-+ML_HOME=/usr/bin
-+ML_SYSTEM=polyml-5.4.0
-+ML_OPTIONS="-H 1000"
-+#ML_SOURCES="$ML_HOME/../src"
- 
- # Poly/ML 32 bit (manual settings)
- #ML_SYSTEM=polyml-5.4.0
-@@ -106,7 +113,7 @@
- ISABELLE_TMP_PREFIX="/tmp/isabelle-$USER"
- 
- # Heap input locations. ML system identifier is included in lookup.
--ISABELLE_PATH="$ISABELLE_HOME_USER/heaps:$ISABELLE_HOME/heaps"
-+ISABELLE_PATH="$ISABELLE_HOME_USER/heaps:/usr/lib64/Isabelle2011-1/heaps"
- 
- # Heap output location. ML system identifier is appended automatically later 
on.
- ISABELLE_OUTPUT="$ISABELLE_HOME_USER/heaps"
-@@ -170,6 +177,7 @@
-   "/usr/local/ProofGeneral" \
-   "/usr/share/ProofGeneral" \
-   "/opt/ProofGeneral" \
-+  "/usr/share/emacs/site-lisp/ProofGeneral" \
-   "")"
- 
- PROOFGENERAL_OPTIONS=""

diff --git a/sci-mathematics/isabelle/files/isabelle-2011.1-graphbrowser.patch 
b/sci-mathematics/isabelle/files/isabelle-2011.1-graphbrowser.patch
deleted file mode 100644
index ed8036a..0000000
--- a/sci-mathematics/isabelle/files/isabelle-2011.1-graphbrowser.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- Isabelle2011-1-orig/lib/browser/build      2011-10-10 01:47:58.000000000 
+1100
-+++ Isabelle2011-1/lib/browser/build   2012-01-08 12:58:06.041444651 +1100
-@@ -6,6 +6,8 @@
- #
- # Requires proper Isabelle settings environment.
- 
-+ISABELLE_HOME="$(cd "$(dirname "${0}")/../.."; pwd -P)"
-+source "$ISABELLE_HOME/lib/scripts/getsettings" || exit 2
- 
- ## diagnostics
- 

diff --git a/sci-mathematics/isabelle/files/isabelle-2011.1-libsha1.patch 
b/sci-mathematics/isabelle/files/isabelle-2011.1-libsha1.patch
deleted file mode 100644
index 905a1eb..0000000
--- a/sci-mathematics/isabelle/files/isabelle-2011.1-libsha1.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- Isabelle2011-1-orig/src/Pure/General/sha1_polyml.ML        2011-10-10 
01:47:58.000000000 +1100
-+++ Isabelle2011-1/src/Pure/General/sha1_polyml.ML     2012-12-05 
23:28:15.004733643 +1100
-@@ -18,7 +18,7 @@
-   in (op ^) (pairself hex_digit (Integer.div_mod (Char.ord c) 16)) end
- 
- val lib_path =
--  ("$ML_HOME/" ^ (if ML_System.platform_is_cygwin then "sha1.dll" else 
"libsha1.so"))
-+  ("$SHA1_HOME/" ^ (if ML_System.platform_is_cygwin then "sha1.dll" else 
"libsha1.so"))
-   |> Path.explode;
- 
- fun digest_external str =

diff --git 
a/sci-mathematics/isabelle/files/isabelle-2011.1-proofgeneral-gentoo-path.patch 
b/sci-mathematics/isabelle/files/isabelle-2011.1-proofgeneral-gentoo-path.patch
deleted file mode 100644
index 67e3476..0000000
--- 
a/sci-mathematics/isabelle/files/isabelle-2011.1-proofgeneral-gentoo-path.patch
+++ /dev/null
@@ -1,39 +0,0 @@
---- Isabelle2011-1-orig/etc/settings   2011-10-10 01:47:58.000000000 +1100
-+++ Isabelle2011-1/etc/settings        2012-01-01 16:33:27.922565527 +1100
-@@ -24,9 +24,16 @@
-   "/usr/share/polyml/$ML_PLATFORM" \
-   "/opt/polyml/$ML_PLATFORM" \
-   "")"
--ML_SYSTEM=$("$ISABELLE_HOME/lib/scripts/polyml-version")
--ML_OPTIONS="-H 200"
--ML_SOURCES="$ML_HOME/../src"
-+# ML_SYSTEM=$("$ISABELLE_HOME/lib/scripts/polyml-version")
-+# ML_OPTIONS="-H 200"
-+# ML_SOURCES="$ML_HOME/../src"
-+
-+# Poly/ML 5.4.0 (64 bit)
-+ML_PLATFORM=x86_64-linux
-+ML_HOME=/usr/bin
-+ML_SYSTEM=polyml-5.4.0
-+ML_OPTIONS="-H 1000"
-+#ML_SOURCES="$ML_HOME/../src"
- 
- # Poly/ML 32 bit (manual settings)
- #ML_SYSTEM=polyml-5.4.0
-@@ -106,7 +113,7 @@
- ISABELLE_TMP_PREFIX="/tmp/isabelle-$USER"
- 
- # Heap input locations. ML system identifier is included in lookup.
--ISABELLE_PATH="$ISABELLE_HOME_USER/heaps:$ISABELLE_HOME/heaps"
-+ISABELLE_PATH="$ISABELLE_HOME_USER/heaps:/usr/lib64/Isabelle2011-1/heaps"
- 
- # Heap output location. ML system identifier is appended automatically later 
on.
- ISABELLE_OUTPUT="$ISABELLE_HOME_USER/heaps"
-@@ -170,6 +177,7 @@
-   "/usr/local/ProofGeneral" \
-   "/usr/share/ProofGeneral" \
-   "/opt/ProofGeneral" \
-+  "/usr/share/emacs/site-lisp/ProofGeneral" \
-   "")"
- 
- PROOFGENERAL_OPTIONS=""

diff --git 
a/sci-mathematics/isabelle/files/isabelle-2011.1-reverse-line-editor-order.patch
 
b/sci-mathematics/isabelle/files/isabelle-2011.1-reverse-line-editor-order.patch
deleted file mode 100644
index b2f2c35..0000000
--- 
a/sci-mathematics/isabelle/files/isabelle-2011.1-reverse-line-editor-order.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- Isabelle2011-1-orig/etc/settings   2011-10-10 01:47:58.000000000 +1100
-+++ Isabelle2011-1/etc/settings        2012-05-27 23:28:37.283028668 +1000
-@@ -66,8 +66,8 @@
- ###
- 
- ISABELLE_LINE_EDITOR=""
--[ -z "$ISABELLE_LINE_EDITOR" ] && ISABELLE_LINE_EDITOR="$(type -p rlwrap)"
- [ -z "$ISABELLE_LINE_EDITOR" ] && ISABELLE_LINE_EDITOR="$(type -p ledit)"
-+[ -z "$ISABELLE_LINE_EDITOR" ] && ISABELLE_LINE_EDITOR="$(type -p rlwrap)"
- 
- 
- ###

diff --git a/sci-mathematics/isabelle/files/isabelle-2012-gentoo-settings.patch 
b/sci-mathematics/isabelle/files/isabelle-2012-gentoo-settings.patch
deleted file mode 100644
index 8994491..0000000
--- a/sci-mathematics/isabelle/files/isabelle-2012-gentoo-settings.patch
+++ /dev/null
@@ -1,62 +0,0 @@
---- Isabelle2012-orig/etc/settings     2012-05-23 03:07:38.000000000 +1000
-+++ Isabelle2012/etc/settings  2012-05-27 18:07:26.502878614 +1000
-@@ -16,17 +16,24 @@
- # Only one of the sections below should be activated.
- 
- # Poly/ML default (automated settings)
--ML_PLATFORM="$ISABELLE_PLATFORM"
--ML_HOME="$(choosefrom \
--  "$ISABELLE_HOME/contrib/polyml/$ML_PLATFORM" \
--  "$ISABELLE_HOME/../polyml/$ML_PLATFORM" \
--  "/usr/local/polyml/$ML_PLATFORM" \
--  "/usr/share/polyml/$ML_PLATFORM" \
--  "/opt/polyml/$ML_PLATFORM" \
--  "")"
--ML_SYSTEM=$("$ISABELLE_HOME/lib/scripts/polyml-version")
--ML_OPTIONS="-H 200"
--ML_SOURCES="$ML_HOME/../src"
-+# ML_PLATFORM="$ISABELLE_PLATFORM"
-+# ML_HOME="$(choosefrom \
-+#   "$ISABELLE_HOME/contrib/polyml/$ML_PLATFORM" \
-+#   "$ISABELLE_HOME/../polyml/$ML_PLATFORM" \
-+#   "/usr/local/polyml/$ML_PLATFORM" \
-+#   "/usr/share/polyml/$ML_PLATFORM" \
-+#   "/opt/polyml/$ML_PLATFORM" \
-+#   "")"
-+# ML_SYSTEM=$("$ISABELLE_HOME/lib/scripts/polyml-version")
-+# ML_OPTIONS="-H 200"
-+# ML_SOURCES="$ML_HOME/../src"
-+
-+# Poly/ML Gentoo (x86_64)
-+ML_PLATFORM=x86_64-linux
-+ML_HOME="/usr/bin"
-+ML_SYSTEM=polyml-5.4.0
-+ML_OPTIONS="-H 1000"
-+ML_SOURCES="/usr/src/debug/dev-lang/polyml-5.4.0"
- 
- # Poly/ML 32 bit (manual settings)
- #ML_SYSTEM=polyml-5.4.1
-@@ -102,7 +109,7 @@
- ISABELLE_TMP_PREFIX="/tmp/isabelle-$USER"
- 
- # Heap input locations. ML system identifier is included in lookup.
--ISABELLE_PATH="$ISABELLE_HOME_USER/heaps:$ISABELLE_HOME/heaps"
-+ISABELLE_PATH="$ISABELLE_HOME_USER/heaps:/usr/lib64/Isabelle2012/heaps"
- 
- # Heap output location. ML system identifier is appended automatically later 
on.
- ISABELLE_OUTPUT="$ISABELLE_HOME_USER/heaps"
-@@ -161,13 +168,7 @@
- ###
- 
- # Proof General home, look in a variety of places
--PROOFGENERAL_HOME="$(choosefrom \
--  "$ISABELLE_HOME/contrib/ProofGeneral" \
--  "$ISABELLE_HOME/../ProofGeneral" \
--  "/usr/local/ProofGeneral" \
--  "/usr/share/ProofGeneral" \
--  "/opt/ProofGeneral" \
--  "")"
-+PROOFGENERAL_HOME="/usr/share/emacs/site-lisp/ProofGeneral"
- 
- PROOFGENERAL_OPTIONS=""
- #PROOFGENERAL_OPTIONS="-m no_brackets -m no_type_brackets"

diff --git 
a/sci-mathematics/isabelle/files/isabelle-2012-redundant-equations-in-function-definitions-error.patch
 
b/sci-mathematics/isabelle/files/isabelle-2012-redundant-equations-in-function-definitions-error.patch
deleted file mode 100644
index 18ae43d..0000000
--- 
a/sci-mathematics/isabelle/files/isabelle-2012-redundant-equations-in-function-definitions-error.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-diff -r dd611ab202a8 -r e7e647949c95 src/HOL/Tools/Function/fun.ML
---- a/src/HOL/Tools/Function/fun.ML    Wed Jun 06 10:35:05 2012 +0200
-+++ b/src/HOL/Tools/Function/fun.ML    Wed Jun 06 21:36:21 2012 +0200
-@@ -84,10 +84,10 @@
-     spec @ mk_catchall fixes arity_of
-   end
- 
--fun warnings ctxt origs tss =
-+fun further_checks ctxt origs tss =
-   let
--    fun warn_redundant t =
--      warning ("Ignoring redundant equation: " ^ quote (Syntax.string_of_term 
ctxt t))
-+    fun fail_redundant t =
-+      error (cat_lines ["Equation is redundant (covered by preceding 
clauses):", Syntax.string_of_term ctxt t])
-     fun warn_missing strs =
-       warning (cat_lines ("Missing patterns in function definition:" :: strs))
- 
-@@ -100,7 +100,7 @@
-          @ ["(" ^ string_of_int (length rest) ^ " more)"])
- 
-     val _ = (origs ~~ tss')
--      |> map (fn (t, ts) => if null ts then warn_redundant t else ())
-+      |> map (fn (t, ts) => if null ts then fail_redundant t else ())
-   in
-     ()
-   end
-@@ -119,7 +119,7 @@
-       val compleqs = add_catchall ctxt fixes feqs (* Completion *)
- 
-       val spliteqs = Function_Split.split_all_equations ctxt compleqs
--        |> tap (warnings ctxt feqs)
-+        |> tap (further_checks ctxt feqs)
- 
-       fun restore_spec thms =
-         bnds ~~ take (length bnds) (unflat spliteqs thms)

diff --git a/sci-mathematics/isabelle/files/isabelle-2012-signal-handling.patch 
b/sci-mathematics/isabelle/files/isabelle-2012-signal-handling.patch
deleted file mode 100644
index d238f41..0000000
--- a/sci-mathematics/isabelle/files/isabelle-2012-signal-handling.patch
+++ /dev/null
@@ -1,8 +0,0 @@
-diff -r c79adcae9869 -r 6de952f4069f lib/scripts/run-polyml
---- a/lib/scripts/run-polyml   Fri May 25 13:23:43 2012 +0200
-+++ b/lib/scripts/run-polyml   Fri May 25 17:14:14 2012 +0200
-@@ -76,3 +76,3 @@
-  "$ISABELLE_HOME/lib/scripts/feeder" -p -h "$MLTEXT" -t "$MLEXIT" 
$FEEDER_OPTS | \
--  { read FPID; "$POLY" -q $ML_OPTIONS; RC="$?"; kill -HUP "$FPID"; exit 
"$RC"; }
-+  { read FPID; "$POLY" -q $ML_OPTIONS; RC="$?"; kill -TERM "$FPID"; exit 
"$RC"; }
-  RC="$?"

diff --git 
a/sci-mathematics/isabelle/files/isabelle-2013-HOL-Predicate_Compile_Examples.patch
 
b/sci-mathematics/isabelle/files/isabelle-2013-HOL-Predicate_Compile_Examples.patch
deleted file mode 100644
index bce7eec..0000000
--- 
a/sci-mathematics/isabelle/files/isabelle-2013-HOL-Predicate_Compile_Examples.patch
+++ /dev/null
@@ -1,82 +0,0 @@
---- 
Isabelle2013-orig/src/HOL/Predicate_Compile_Examples/Hotel_Example_Prolog.thy   
   2013-02-13 00:31:10.000000000 +1100
-+++ Isabelle2013/src/HOL/Predicate_Compile_Examples/Hotel_Example_Prolog.thy   
2013-08-31 14:37:02.015159000 +1000
-@@ -82,7 +82,7 @@
- setup {* Context.theory_map (Quickcheck.add_tester ("prolog", 
(Code_Prolog.active, Code_Prolog.test_goals))) *}
- 
- lemma "\<lbrakk> hotel s; isinp s r g \<rbrakk> \<Longrightarrow> owns s r = 
Some g"
--quickcheck[tester = prolog, iterations = 1, expect = counterexample]
-+quickcheck[tester = prolog, iterations = 1]
- oops
- 
- section {* Manual setup to find the counterexample *}
-@@ -110,7 +110,7 @@
- 
- lemma
-   "hotel s ==> feels_safe s r ==> isinp s r g ==> owns s r = Some g"
--quickcheck[tester = prolog, iterations = 1, expect = counterexample]
-+quickcheck[tester = prolog, iterations = 1]
- oops
- 
- section {* Using a global limit for limiting the execution *} 
-@@ -146,7 +146,7 @@
- 
- lemma
-   "hotel s ==> feels_safe s r ==> isinp s r g ==> owns s r = Some g"
--quickcheck[tester = prolog, iterations = 1, expect = counterexample]
-+quickcheck[tester = prolog, iterations = 1]
- oops
- 
- end
-\ No newline at end of file
---- 
Isabelle2013-orig/src/HOL/Predicate_Compile_Examples/Context_Free_Grammar_Example.thy
      2013-02-13 00:31:10.000000000 +1100
-+++ 
Isabelle2013/src/HOL/Predicate_Compile_Examples/Context_Free_Grammar_Example.thy
   2013-08-31 14:36:47.049851000 +1000
-@@ -33,7 +33,7 @@
- 
- lemma
-   "S\<^isub>1p w \<Longrightarrow> w = []"
--quickcheck[tester = prolog, iterations=1, expect = counterexample]
-+quickcheck[tester = prolog, iterations=1]
- oops
- 
- definition "filter_a = filter (\<lambda>x. x = a)"
-@@ -67,7 +67,7 @@
- 
- theorem S\<^isub>1_sound:
- "S\<^isub>1p w \<Longrightarrow> length [x \<leftarrow> w. x = a] = length [x 
\<leftarrow> w. x = b]"
--quickcheck[tester = prolog, iterations=1, expect = counterexample]
-+quickcheck[tester = prolog, iterations=1]
- oops
- 
- 
-@@ -91,7 +91,7 @@
- 
- theorem S\<^isub>2_sound:
-   "S\<^isub>2p w \<longrightarrow> length [x \<leftarrow> w. x = a] = length 
[x \<leftarrow> w. x = b]"
--quickcheck[tester = prolog, iterations=1, expect = counterexample]
-+quickcheck[tester = prolog, iterations=1]
- oops
- 
- inductive_set S\<^isub>3 and A\<^isub>3 and B\<^isub>3 where
---- Isabelle2013-orig/src/HOL/Predicate_Compile_Examples/Lambda_Example.thy    
2013-02-13 00:31:10.000000000 +1100
-+++ Isabelle2013/src/HOL/Predicate_Compile_Examples/Lambda_Example.thy 
2013-08-31 14:28:11.784390000 +1000
-@@ -92,7 +92,7 @@
- 
- lemma
-   "\<Gamma> \<turnstile> t : U \<Longrightarrow> t 
\<rightarrow>\<^sub>\<beta> t' \<Longrightarrow> \<Gamma> \<turnstile> t' : U"
--quickcheck[tester = prolog, iterations = 1, expect = counterexample]
-+quickcheck[tester = prolog, iterations = 1]
- oops
- 
- text {* Verifying that the found counterexample really is one by means of a 
proof *}
---- Isabelle2013-orig/src/HOL/Predicate_Compile_Examples/List_Examples.thy     
2013-02-13 00:31:10.000000000 +1100
-+++ Isabelle2013/src/HOL/Predicate_Compile_Examples/List_Examples.thy  
2013-08-31 14:27:52.013962000 +1000
-@@ -21,7 +21,7 @@
- lemma "(xs :: nat list) = ys @ ys --> rev xs = xs"
- quickcheck[tester = random, iterations = 10000]
- quickcheck[tester = smart_exhaustive, iterations = 1, expect = counterexample]
--quickcheck[tester = prolog, expect = counterexample]
-+quickcheck[tester = prolog]
- oops
- 
- end
-\ No newline at end of file

diff --git a/sci-mathematics/isabelle/files/isabelle-2013-classpath.patch 
b/sci-mathematics/isabelle/files/isabelle-2013-classpath.patch
deleted file mode 100644
index e3b2271..0000000
--- a/sci-mathematics/isabelle/files/isabelle-2013-classpath.patch
+++ /dev/null
@@ -1,149 +0,0 @@
---- Isabelle2013-orig/lib/Tools/java   2013-02-13 00:31:02.000000000 +1100
-+++ Isabelle2013/lib/Tools/java        2015-04-17 12:16:04.734716358 +1000
-@@ -6,5 +6,5 @@
- 
- CLASSPATH="$(jvmpath "$CLASSPATH")"
- isabelle_jdk java -Dfile.encoding=UTF-8 -server \
--  "-Djava.ext.dirs=$(jvmpath 
"$ISABELLE_JAVA_EXT:$ISABELLE_HOME/lib/classes/ext")" "$@"
-+  "-Djava.ext.dirs=$(jvmpath 
"$ISABELLE_JAVA_EXT:$ISABELLE_HOME/lib/classes/ext:$(java-config -p scala-2.10 
| sed 's@\([^:]*\)/[^:]*:.*@\1@')")" "$@"
- 
---- Isabelle2013-orig/lib/Tools/scala  2013-02-13 00:31:02.000000000 +1100
-+++ Isabelle2013/lib/Tools/scala       2015-04-17 12:12:21.606890256 +1000
-@@ -8,4 +8,4 @@
- 
- CLASSPATH="$(jvmpath "$CLASSPATH")"
- isabelle_scala scala -Dfile.encoding=UTF-8 \
--  "-Djava.ext.dirs=$(jvmpath 
"$ISABELLE_JAVA_EXT:$ISABELLE_HOME/lib/classes/ext")" "$@"
-+  "-Djava.ext.dirs=$(jvmpath 
"$ISABELLE_JAVA_EXT:$ISABELLE_HOME/lib/classes/ext:$(java-config -p scala-2.10 
| sed 's@\([^:]*\)/[^:]*:.*@\1@')")" "$@"
---- Isabelle2013-orig/lib/Tools/scalac 2013-02-13 00:31:02.000000000 +1100
-+++ Isabelle2013/lib/Tools/scalac      2015-04-17 12:12:36.895871214 +1000
-@@ -8,5 +8,5 @@
- 
- CLASSPATH="$(jvmpath "$CLASSPATH")"
- isabelle_scala scalac -Dfile.encoding=UTF-8 \
--  "-Djava.ext.dirs=$(jvmpath 
"$ISABELLE_JAVA_EXT:$ISABELLE_HOME/lib/classes/ext")" "$@"
-+  "-Djava.ext.dirs=$(jvmpath 
"$ISABELLE_JAVA_EXT:$ISABELLE_HOME/lib/classes/ext:$(java-config -p scala-2.10 
| sed 's@\([^:]*\)/[^:]*:.*@\1@')")" "$@"
- 
---- Isabelle2013-orig/src/Pure/build-jars      2013-02-13 00:31:15.000000000 
+1100
-+++ Isabelle2013/src/Pure/build-jars   2013-08-18 12:55:51.400924000 +1000
-@@ -133,7 +133,7 @@
- declare -a JFREECHART_JARS=()
- for NAME in $JFREECHART_JAR_NAMES
- do
--  JFREECHART_JARS["${#JFREECHART_JARS[@]}"]="$JFREECHART_HOME/lib/$NAME"
-+  JFREECHART_JARS["${#JFREECHART_JARS[@]}"]="$NAME"
- done
- 
- 
---- Isabelle2013-orig/src/Tools/jEdit/lib/Tools/jedit  2013-02-13 
00:31:16.000000000 +1100
-+++ Isabelle2013/src/Tools/jEdit/lib/Tools/jedit       2013-08-18 
16:39:15.495244000 +1000
-@@ -214,97 +214,11 @@
- declare -a JFREECHART_JARS=()
- for NAME in $JFREECHART_JAR_NAMES
- do
--  JFREECHART_JARS["${#JFREECHART_JARS[@]}"]="$JFREECHART_HOME/lib/$NAME"
-+  JFREECHART_JARS["${#JFREECHART_JARS[@]}"]="$NAME"
- done
- 
--
--# target
--
--TARGET="dist/jars/Isabelle-jEdit.jar"
--
--declare -a UPDATED=()
--
--if [ "$BUILD_JARS" = jars_fresh ]; then
--  OUTDATED=true
--else
--  OUTDATED=false
--  if [ ! -e "$TARGET" ]; then
--    OUTDATED=true
--  else
--    if [ -n "$ISABELLE_JEDIT_BUILD_HOME" ]; then
--      declare -a DEPS=(
--        "$JEDIT_JAR" "${JEDIT_JARS[@]}" "${JFREECHART_JARS[@]}"
--        "$PURE_JAR" "$GRAPHVIEW_JAR" "${SOURCES[@]}" "${RESOURCES[@]}"
--      )
--    elif [ -e "$ISABELLE_HOME/Admin/build" ]; then
--      declare -a DEPS=("$PURE_JAR" "$GRAPHVIEW_JAR" "${SOURCES[@]}" 
"${RESOURCES[@]}")
--    else
--      declare -a DEPS=()
--    fi
--    for DEP in "${DEPS[@]}"
--    do
--      [ ! -e "$DEP" ] && fail "Missing file: $DEP"
--      [ "$DEP" -nt "$TARGET" ] && {
--        OUTDATED=true
--        UPDATED["${#UPDATED[@]}"]="$DEP"
--      }
--    done
--  fi
--fi
--
--
--# build
--
--if [ "$OUTDATED" = true ]
--then
--  echo "### Building Isabelle/jEdit ..."
--
--  [ "${#UPDATED[@]}" -gt 0 ] && {
--    echo "Changed files:"
--    for FILE in "${UPDATED[@]}"
--    do
--      echo "  $FILE"
--    done
--  }
--
--  [ -z "$ISABELLE_JEDIT_BUILD_HOME" ] && \
--    fail "Unknown ISABELLE_JEDIT_BUILD_HOME -- missing auxiliary component"
--
--  rm -rf dist || failed
--  mkdir -p dist dist/classes || failed
--
--  cp -p -R -f 
"$ISABELLE_JEDIT_BUILD_HOME/contrib/$ISABELLE_JEDIT_BUILD_VERSION/." dist/.
--  cp -p -R -f "${RESOURCES[@]}" dist/classes/.
--  cp src/jEdit.props dist/properties/.
--  cp -p -R -f src/modes/. dist/modes/.
--
--  perl -i -e 'while (<>) {
--    if (m/NAME="javacc"/) {
--      print qq,<MODE NAME="isabelle" FILE="isabelle.xml" 
FILE_NAME_GLOB="*.thy"/>\n\n,;
--      print qq,<MODE NAME="isabelle-options" 
FILE="isabelle-options.xml"/>\n\n,;
--      print qq,<MODE NAME="isabelle-root" FILE="isabelle-root.xml" 
FILE_NAME_GLOB="ROOT"/>\n\n,; }
--    print; }' dist/modes/catalog
--
--  cp -p -R -f "${JEDIT_JARS[@]}" dist/jars/. || failed
--  (
--    for JAR in "$JEDIT_JAR" "${JEDIT_JARS[@]}" "${JFREECHART_JARS[@]}" 
"$PURE_JAR" \
--      "$GRAPHVIEW_JAR" "$SCALA_HOME/lib/scala-compiler.jar"
--    do
--      CLASSPATH="$CLASSPATH:$JAR"
--    done
--    CLASSPATH="$(jvmpath "$CLASSPATH")"
--    exec "$SCALA_HOME/bin/scalac" $ISABELLE_SCALA_BUILD_OPTIONS -d 
dist/classes "${SOURCES[@]}"
--  ) || fail "Failed to compile sources"
--
--  cd dist/classes
--  isabelle_jdk jar cf "../jars/Isabelle-jEdit.jar" * || failed
--  cd ../..
--  rm -rf dist/classes
--fi
--
- popd >/dev/null
- 
--
- ## main
- 
- if [ "$BUILD_ONLY" = false ]; then
---- Isabelle2013-orig/contrib/jfreechart-1.0.14/etc/settings   2012-12-09 
07:23:53.000000000 +1100
-+++ Isabelle2013/contrib/jfreechart-1.0.14/etc/settings        2013-08-18 
16:18:10.244698000 +1000
-@@ -1,7 +1,5 @@
- # -*- shell-script -*- :mode=shellscript:
- 
- JFREECHART_HOME="$COMPONENT"
--JFREECHART_JAR_NAMES="iText-2.1.5.jar jcommon-1.0.18.jar 
jfreechart-1.0.14.jar"
--
--ISABELLE_JAVA_EXT="$ISABELLE_JAVA_EXT:$JFREECHART_HOME/lib"
-+JFREECHART_JAR_NAMES="$(java-config -p itext | sed -e 's@:@ @g') 
$(java-config -p jcommon-1.0 | sed -e 's@:@ @g') $(java-config -p 
jfreechart-1.0 | sed -e 's@:@ @g')"
- 

diff --git a/sci-mathematics/isabelle/files/isabelle-2013.2-classpath.patch 
b/sci-mathematics/isabelle/files/isabelle-2013.2-classpath.patch
deleted file mode 100644
index b3ad4ae..0000000
--- a/sci-mathematics/isabelle/files/isabelle-2013.2-classpath.patch
+++ /dev/null
@@ -1,135 +0,0 @@
---- Isabelle2013-2-orig/lib/Tools/java 2013-12-06 02:18:34.000000000 +1100
-+++ Isabelle2013-2/lib/Tools/java      2015-04-17 12:23:11.535463796 +1000
-@@ -10,5 +10,5 @@
- unset CLASSPATH
- 
- isabelle_jdk java "${JAVA_ARGS[@]}" \
--  -classpath "$(jvmpath "$ISABELLE_CLASSPATH")" "$@"
-+  -classpath "$(jvmpath "$ISABELLE_CLASSPATH:$(java-config -p scala-2.11 | 
sed 's@\([^:]*\)/[^:]*:.*@\1@')")" "$@"
- 
---- Isabelle2013-2-orig/lib/Tools/scala        2013-12-06 02:18:34.000000000 
+1100
-+++ Isabelle2013-2/lib/Tools/scala     2015-04-17 12:23:24.836455672 +1000
-@@ -7,5 +7,5 @@
- isabelle_admin_build jars || exit $?
- 
- isabelle_scala scala -Dfile.encoding=UTF-8 \
--  -classpath "$(jvmpath "$ISABELLE_CLASSPATH")" "$@"
-+  -classpath "$(jvmpath "$ISABELLE_CLASSPATH:$(java-config -p scala-2.11 | 
sed 's@\([^:]*\)/[^:]*:.*@\1@')")" "$@"
- 
---- Isabelle2013-2-orig/lib/Tools/scalac       2013-12-06 02:18:34.000000000 
+1100
-+++ Isabelle2013-2/lib/Tools/scalac    2015-04-17 12:23:33.084450628 +1000
-@@ -7,5 +7,5 @@
- isabelle_admin_build jars || exit $?
- 
- isabelle_scala scalac -Dfile.encoding=UTF-8 \
--  -classpath "$(jvmpath "$ISABELLE_CLASSPATH")" "$@"
-+  -classpath "$(jvmpath "$ISABELLE_CLASSPATH:$(java-config -p scala-2.11 | 
sed 's@\([^:]*\)/[^:]*:.*@\1@')")" "$@"
- 
---- Isabelle2013-2-orig/src/Tools/jEdit/lib/Tools/jedit        2013-12-06 
02:19:04.000000000 +1100
-+++ Isabelle2013-2/src/Tools/jEdit/lib/Tools/jedit     2014-02-09 
20:59:14.026841490 +1100
-@@ -211,105 +211,6 @@
-   "$ISABELLE_JEDIT_BUILD_HOME/contrib/jsr305-2.0.0.jar"
- )
- 
--
--# target
--
--TARGET="dist/jars/Isabelle-jEdit.jar"
--
--declare -a UPDATED=()
--
--if [ "$BUILD_JARS" = jars_fresh ]; then
--  OUTDATED=true
--else
--  OUTDATED=false
--  if [ ! -e "$TARGET" ]; then
--    OUTDATED=true
--  else
--    if [ -n "$ISABELLE_JEDIT_BUILD_HOME" ]; then
--      declare -a DEPS=(
--        "$JEDIT_JAR" "${JEDIT_JARS[@]}" "$PURE_JAR" "$GRAPHVIEW_JAR"
--        "${SOURCES[@]}" "${RESOURCES[@]}"
--      )
--    elif [ -e "$ISABELLE_HOME/Admin/build" ]; then
--      declare -a DEPS=("$PURE_JAR" "$GRAPHVIEW_JAR" "${SOURCES[@]}" 
"${RESOURCES[@]}")
--    else
--      declare -a DEPS=()
--    fi
--    for DEP in "${DEPS[@]}"
--    do
--      [ ! -e "$DEP" ] && fail "Missing file: $DEP"
--      [ "$DEP" -nt "$TARGET" ] && {
--        OUTDATED=true
--        UPDATED["${#UPDATED[@]}"]="$DEP"
--      }
--    done
--  fi
--fi
--
--
--# build
--
--if [ "$OUTDATED" = true ]
--then
--  echo "### Building Isabelle/jEdit ..."
--
--  [ "${#UPDATED[@]}" -gt 0 ] && {
--    echo "Changed files:"
--    for FILE in "${UPDATED[@]}"
--    do
--      echo "  $FILE"
--    done
--  }
--
--  [ -z "$ISABELLE_JEDIT_BUILD_HOME" ] && \
--    fail "Unknown ISABELLE_JEDIT_BUILD_HOME -- missing auxiliary component"
--
--  rm -rf dist || failed
--  mkdir -p dist dist/classes || failed
--
--  cp -p -R -f 
"$ISABELLE_JEDIT_BUILD_HOME/contrib/$ISABELLE_JEDIT_BUILD_VERSION/." dist/.
--  cp -p -R -f "${RESOURCES[@]}" dist/classes/.
--  cp src/jEdit.props dist/properties/.
--  cp -p -R -f src/modes/. dist/modes/.
--
--  perl -i -e 'while (<>) {
--    if (m/NAME="javacc"/) {
--      print qq,<MODE NAME="isabelle" FILE="isabelle.xml" 
FILE_NAME_GLOB="*.thy"/>\n\n,;
--      print qq,<MODE NAME="isabelle-news" FILE="isabelle-news.xml"/>\n\n,;
--      print qq,<MODE NAME="isabelle-options" 
FILE="isabelle-options.xml"/>\n\n,;
--      print qq,<MODE NAME="isabelle-root" FILE="isabelle-root.xml" 
FILE_NAME_GLOB="ROOT"/>\n\n,; }
--    print; }' dist/modes/catalog
--
--  cd dist
--  isabelle_jdk jar xf jedit.jar
--  cp "$ISABELLE_HOME/lib/logo/isabelle-32.gif" \
--    "org/gjt/sp/jedit/icons/themes/classic/32x32/apps/isabelle.gif" || failed
--  cp "$ISABELLE_HOME/lib/logo/isabelle-32.gif" \
--    "org/gjt/sp/jedit/icons/themes/tango/32x32/apps/isabelle.gif" || failed
--  isabelle_jdk jar cfe jedit.jar org.gjt.sp.jedit.jEdit org || failed
--  rm -rf META-INF org
--  cd ..
--
--  cp -p -R -f "${JEDIT_JARS[@]}" dist/jars/. || failed
--  (
--    #workaround for scalac 2.10.2
--    function stty() { :; }
--    export -f stty
--
--    for JAR in "$JEDIT_JAR" "${JEDIT_JARS[@]}" "$PURE_JAR" "$GRAPHVIEW_JAR"
--    do
--      classpath "$JAR"
--    done
--    export CLASSPATH="$(jvmpath "$ISABELLE_CLASSPATH")"
--    exec "$SCALA_HOME/bin/scalac" $ISABELLE_SCALA_BUILD_OPTIONS -d 
dist/classes "${SOURCES[@]}"
--  ) || fail "Failed to compile sources"
--
--  cd dist/classes
--  isabelle_jdk jar cf "../jars/Isabelle-jEdit.jar" * || failed
--  cd ../..
--  rm -rf dist/classes
--fi
--
- popd >/dev/null
- 
- 

diff --git a/sci-mathematics/isabelle/isabelle-2011.1-r2.ebuild 
b/sci-mathematics/isabelle/isabelle-2011.1-r2.ebuild
deleted file mode 100644
index 6b96bcb..0000000
--- a/sci-mathematics/isabelle/isabelle-2011.1-r2.ebuild
+++ /dev/null
@@ -1,254 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="5"
-
-inherit eutils java-pkg-2 multilib versionator
-
-MY_PN="Isabelle"
-MY_PV=$(replace_all_version_separators '-')
-MY_P="${MY_PN}${MY_PV}"
-
-DESCRIPTION="Isabelle is a generic proof assistant"
-HOMEPAGE="http://www.cl.cam.ac.uk/research/hvg/isabelle/index.html";
-SRC_URI="http://www.cl.cam.ac.uk/research/hvg/isabelle/dist/${MY_P}.tar.gz";
-
-LICENSE="BSD"
-SLOT="0/${PV}"
-KEYWORDS="~amd64 ~x86"
-ALL_LOGICS="Pure FOL +HOL ZF CCL CTT Cube FOLP LCF Sequents"
-IUSE="${ALL_LOGICS} doc graphbrowsing ledit readline +proofgeneral test"
-
-#upstream says
-#bash 2.x/3.x, Poly/ML 5.x, Perl 5.x,
-#for document preparation: complete LaTeX
-DEPEND=">=app-shells/bash-3.0:*
-               >=dev-lang/polyml-5.4.1:=[-portable]
-               >=dev-lang/perl-5.8.8-r2"
-
-RDEPEND="dev-perl/libwww-perl
-       sci-mathematics/sha1-polyml
-       doc? (
-               virtual/latex-base
-               dev-tex/rail
-       )
-       proofgeneral? (
-               app-emacs/proofgeneral
-       )
-       ledit? (
-               app-misc/ledit
-       )
-       readline? (
-               app-misc/rlwrap
-       )
-       ${DEPEND}"
-
-S="${WORKDIR}"/Isabelle${MY_PV}
-TARGETDIR="/usr/share/Isabelle"${MY_PV}
-LIBDIR="/usr/"$(get_libdir)"/Isabelle"${MY_PV}
-
-pkg_setup() {
-       java-pkg-2_pkg_setup
-       if ! use proofgeneral
-       then
-               ewarn "You have deselected the Proof General interface."
-               ewarn "Only a text terminal will be installed."
-               ewarn "Emerge Isabelle with the proofgeneral USE flag enabled"
-               ewarn "to get the common interface, that most people want."
-       fi
-}
-
-src_prepare() {
-       java-pkg-2_src_prepare
-       epatch "${FILESDIR}/${PN}-2011.1-gentoo-settings.patch"
-       polymlver=$(poly -v | cut -d' ' -f2)
-       polymlarch=$(poly -v | cut -d' ' -f9 | cut -d'-' -f1)
-       sed -e "s@5.4.0@${polymlver}@g" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure polyml version in etc/settings"
-       sed -e "s@ML_HOME=\"/@ML_HOME=\"${ROOT}@" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure polyml ML_HOME in etc/settings"
-       sed -e "s@x86_64@${polymlarch}@g" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure polyml arch in etc/settings"
-       sed -e "s@PROOFGENERAL_HOME=\"/@PROOFGENERAL_HOME=\"${ROOT}@" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure PROOFGENERAL_HOME in etc/settings"
-       sed -e "s@/usr/lib64/Isabelle${MY_PV}@${LIBDIR}@g" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure Isabelle lib directory in 
etc/settings"
-       epatch "${FILESDIR}/${PN}-2011.1-graphbrowser.patch"
-       epatch "${FILESDIR}/${PN}-2011.1-libsha1.patch"
-       cat <<- EOF >> "${S}/etc/settings"
-
-               ISABELLE_GHC="${ROOT}usr/bin/ghc"
-               ISABELLE_OCAML="${ROOT}usr/bin/ocaml"
-               ISABELLE_SWIPL="${ROOT}usr/bin/swipl"
-               ISABELLE_JDK_HOME="\$(java-config --jdk-home)"
-               SCALA_HOME="${ROOT}usr/share/scala"
-               SHA1_HOME="/usr/$(get_libdir)/sha1-polyml"
-       EOF
-       if use ledit && ! use readline; then
-               epatch 
"${FILESDIR}/${PN}-2011.1-reverse-line-editor-order.patch"
-       fi
-}
-
-src_compile() {
-       LOGICS=""
-       for l in "${ALL_LOGICS}"; do
-               if has "${l/+/}"; then
-                       LOGICS="${LOGICS} ${l/+/}"
-               fi
-       done
-       einfo "Building Isabelle logics ${LOGICS}. This may take some time."
-       ./build -b -i "${LOGICS}" || die "building logics failed"
-       ./bin/isabelle makeall || die "isabelle makeall failed"
-       if use graphbrowsing
-       then
-               rm -f "${S}/lib/browser/GraphBrowser.jar" \
-                       || die "failed cleaning graph browser directory"
-               pushd "${S}/lib/browser" \
-                       || die "Could not change directory to lib/browser"
-               ./build || die "failed building the graph browser"
-               popd
-       fi
-}
-
-src_test() {
-       einfo "Running tests. A test run can take up to several hours!"
-       ./build -b -t || die "tests failed"
-}
-
-src_install() {
-       exeinto ${TARGETDIR}/bin
-       doexe bin/isabelle-process bin/isabelle
-
-       insinto ${TARGETDIR}
-       doins -r src
-       doins -r lib
-
-       for i in "./build" \
-               "src/Pure/mk" \
-               "src/Pure/build-jars" \
-               "src/Tools/jEdit/dist/build-support/ci/copy_properties.groovy" \
-               "src/Tools/jEdit/dist/build-support/ci/ci_release.groovy" \
-               "src/Tools/jEdit/lib/Tools/jedit" \
-               "src/Tools/Metis/fix_metis_license" \
-               "src/Tools/Metis/make_metis" \
-               "src/Tools/Metis/scripts/mlpp" \
-               "src/Tools/WWW_Find/lib/Tools/wwwfind" \
-               "src/Tools/Code/lib/Tools/codegen" \
-               "src/HOL/Mirabelle/lib/Tools/mirabelle" \
-               "src/HOL/Tools/Predicate_Compile/lib/scripts/swipl_version" \
-               "src/HOL/Tools/SMT/lib/scripts/remote_smt" \
-               "src/HOL/Tools/ATP/scripts/remote_atp" \
-               "src/HOL/Tools/ATP/scripts/spass" \
-               "src/HOL/Tools/Nitpick/lib/Tools/nitrox" \
-               "src/HOL/Mutabelle/lib/Tools/mutabelle" \
-               "src/HOL/Library/Sum_of_Squares/neos_csdp_client" \
-               "lib/browser/build" \
-               "lib/Tools/tty" \
-               "lib/Tools/mkproject" \
-               "lib/Tools/keywords" \
-               "lib/Tools/browser" \
-               "lib/Tools/install" \
-               "lib/Tools/mkdir" \
-               "lib/Tools/unsymbolize" \
-               "lib/Tools/getenv" \
-               "lib/Tools/java" \
-               "lib/Tools/make" \
-               "lib/Tools/emacs" \
-               "lib/Tools/scala" \
-               "lib/Tools/print" \
-               "lib/Tools/latex" \
-               "lib/Tools/findlogics" \
-               "lib/Tools/doc" \
-               "lib/Tools/logo" \
-               "lib/Tools/usedir" \
-               "lib/Tools/yxml" \
-               "lib/Tools/version" \
-               "lib/Tools/makeall" \
-               "lib/Tools/scalac" \
-               "lib/Tools/document" \
-               "lib/Tools/env" \
-               "lib/Tools/display" \
-               "lib/Tools/dimacs2hol" \
-               "lib/scripts/keywords" \
-               "lib/scripts/unsymbolize" \
-               "lib/scripts/run-polyml" \
-               "lib/scripts/run-smlnj" \
-               "lib/scripts/feeder" \
-               "lib/scripts/java_ext_dirs" \
-               "lib/scripts/yxml" \
-               "lib/scripts/raw_dump" \
-               "lib/scripts/polyml-version" \
-               "lib/scripts/process"
-       do
-               exeinto $(dirname "${TARGETDIR}/${i}")
-               doexe ${i}
-       done
-
-       docompress -x /usr/share/doc/${PF}
-       dodoc -r doc
-       if use doc; then
-               dosym /usr/share/doc/${PF}/doc "${TARGETDIR}/doc"
-       fi
-
-       dodir /etc/isabelle
-       insinto /etc/isabelle
-       doins -r etc/*
-
-       dosym /etc/isabelle "${TARGETDIR}/etc"
-       dosym "${LIBDIR}/heaps" "${TARGETDIR}/heaps"
-
-       insinto ${LIBDIR}
-       doins -r heaps
-
-       bin/isabelle install -d ${TARGETDIR} -p "${ED}usr/bin" \
-               || die "isabelle install failed"
-       newicon lib/icons/isabelle.xpm "${PN}.xpm"
-       dodoc ANNOUNCE CONTRIBUTORS COPYRIGHT NEWS README
-
-       java-pkg_regjar \
-               "${ED}${TARGETDIR}/lib/browser/GraphBrowser.jar" \
-               "${ED}${TARGETDIR}/lib/classes/ext/Pure.jar" \
-               "${ED}${TARGETDIR}/lib/classes/ext/scala-library.jar" \
-               "${ED}${TARGETDIR}/lib/classes/ext/scala-swing.jar" \
-               "${ED}${TARGETDIR}/lib/classes/java_ext_dirs.jar"
-}
-
-pkg_postinst() {
-       # If any of the directories in /etc/isabelle/components do not exist, 
then
-       # even isabelle getenv ISABELLE_HOME fails.  Hence it is necessary to
-       # to delete any non-existing directories.  If an old Isabelle version 
was
-       # installed with component ebuilds like sci-mathematics/e, then the
-       # Isabelle version is upgraded, then the contrib directories will not
-       # exist initially, it is necessary to delete them from 
/etc/isabelle/components.
-       # Then these components are rebuilt (creating these directories) using 
the
-       # EAPI=5 subslot depends.
-       for i in $(egrep '^[^#].*$' "${ROOT}etc/isabelle/components")
-       do
-               if [ ! -d /usr/share/Isabelle2012/${i} ]; then
-                       sed -e "\@${i}@d" -i "${ROOT}etc/isabelle/components"
-               fi
-       done
-       if use ledit && use readline; then
-               elog "Both readline and ledit use flags specified.  The default 
setting"
-               elog "if both are installed is to use readline (rlwrap), this 
can be"
-               elog "modfied by editing the ISABELLE_LINE_EDITOR setting in"
-               elog "${ROOT}/etc/isabelle/settings"
-       fi
-       elog "Please ensure you have a pdf viewer installed, for example:"
-       elog "As root: emerge app-text/zathura-pdf-poppler"
-       elog "Please configure your preferred pdf viewer, something like:"
-       elog "As normal user: xdg-mime default zathura.desktop application/pdf"
-       elog "Or alternatively by editing the PDF_VIEWER variable in the system"
-       elog "settings file ${ROOT}etc/isabelle/settings and/or the user"
-       elog "settings file \$HOME/.isabelle/${MY_P}/etc/settings"
-       elog "To improve sledgehammer performance, consider installing:"
-       elog "USE=isabelle emerge sci-mathematics/e sci-mathematics/spass"
-       elog "For nitpick it is necessary to install:"
-       elog "emerge sci-mathematics/kodkodi"
-}

diff --git a/sci-mathematics/isabelle/isabelle-2011.1.ebuild 
b/sci-mathematics/isabelle/isabelle-2011.1.ebuild
deleted file mode 100644
index f0e0c82..0000000
--- a/sci-mathematics/isabelle/isabelle-2011.1.ebuild
+++ /dev/null
@@ -1,142 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="4"
-
-JAVA_PKG_OPT_USE="graphbrowsing"
-inherit eutils java-pkg-opt-2 multilib versionator
-
-MY_PN="Isabelle"
-MY_PV=$(replace_all_version_separators '-')
-MY_P="${MY_PN}${MY_PV}"
-
-DESCRIPTION="Isabelle is a generic proof assistant"
-HOMEPAGE="http://www.cl.cam.ac.uk/research/hvg/isabelle/index.html";
-SRC_URI="http://www.cl.cam.ac.uk/research/hvg/isabelle/dist/${MY_P}.tar.gz";
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-ALL_LOGICS="Pure FOL +HOL ZF CCL CTT Cube FOLP LCF Sequents"
-IUSE="${ALL_LOGICS} doc graphbrowsing +proofgeneral test"
-
-#upstream says
-#bash 2.x/3.x, Poly/ML 5.x, Perl 5.x,
-#for document preparation: complete LaTeX
-DEPEND=">=app-shells/bash-3.0
-               >=dev-lang/polyml-5.4.1[-portable]
-               >=dev-lang/perl-5.8.8-r2"
-
-RDEPEND="doc? (
-               virtual/latex-base
-               dev-tex/rail
-       )
-       proofgeneral? (
-               app-emacs/proofgeneral
-       )
-       ${DEPEND}"
-
-S="${WORKDIR}"/Isabelle${MY_PV}
-TARGETDIR="/usr/share/Isabelle"${MY_PV}
-LIBDIR="/usr/"$(get_libdir)"/Isabelle"${MY_PV}
-
-pkg_setup() {
-       java-pkg-opt-2_pkg_setup
-       if ! use proofgeneral
-       then
-               ewarn "You have deselected the Proof General interface."
-               ewarn "Only a text terminal will be installed."
-               ewarn "Emerge Isabelle with the proofgeneral USE flag enabled"
-               ewarn "to get the common interface, that most people want."
-       fi
-}
-
-src_prepare() {
-       java-pkg-opt-2_src_prepare
-       if use proofgeneral; then
-               epatch "${FILESDIR}/${PN}-2011.1-proofgeneral-gentoo-path.patch"
-               polymlver=$(poly -v | cut -d' ' -f2)
-               polymlarch=$(poly -v | cut -d' ' -f9 | cut -d'-' -f1)
-               sed -e "s@5.4.0@${polymlver}@g" \
-                       -i "${S}/etc/settings" \
-                       || die "Could not configure polyml version in 
etc/settings"
-               sed -e "s@x86_64@${polymlarch}@g" \
-                       -i "${S}/etc/settings" \
-                       || die "Could not configure polyml arch in etc/settings"
-       fi
-       if use graphbrowsing; then
-               epatch "${FILESDIR}/${PN}-2011.1-graphbrowser.patch"
-       fi
-}
-
-src_compile() {
-       LOGICS=""
-       for l in "${ALL_LOGICS}"; do
-               if has "${l/+/}"; then
-                       LOGICS="${LOGICS} ${l/+/}"
-               fi
-       done
-       einfo "Building Isabelle logics ${LOGICS}. This may take some time."
-       ./build -b -i "${LOGICS}" || die "building logics failed"
-       ./bin/isabelle makeall || die "isabelle makeall failed"
-       if use graphbrowsing
-       then
-               rm -f "${S}/lib/browser/GraphBrowser.jar" \
-                       || die "failed cleaning graph browser directory"
-               pushd "${S}/lib/browser" \
-                       || die "Could not change directory to lib/browser"
-               ./build || die "failed building the graph browser"
-               popd
-       fi
-}
-
-src_test() {
-       einfo "Running tests. A test run can take up to several hours!"
-       ./build -b -t || die "tests failed"
-}
-
-src_install() {
-       exeinto ${TARGETDIR}/bin
-       doexe bin/isabelle-process bin/isabelle
-
-       exeinto ${TARGETDIR}
-       doexe build
-
-       insinto ${TARGETDIR}
-       doins -r src
-       dodoc -r doc
-
-       dodir /etc/isabelle
-       insinto /etc/isabelle
-       doins -r etc/*
-
-       dosym /etc/isabelle "${TARGETDIR}/etc"
-       dosym "${LIBDIR}/heaps" "${TARGETDIR}/heaps"
-
-       insinto ${LIBDIR}
-       doins -r heaps
-
-       # use cp to keep file attributes
-       cp -R lib "${ED}${TARGETDIR}" || die "install lib failed"
-
-       bin/isabelle install -d ${TARGETDIR} -p "${ED}usr/bin" \
-               || die "isabelle install failed"
-       newicon lib/icons/isabelle.xpm "${PN}.xpm"
-       dodoc ANNOUNCE CONTRIBUTORS COPYRIGHT NEWS README
-
-       java-pkg_regjar \
-               "${ED}${TARGETDIR}/lib/browser/GraphBrowser.jar" \
-               "${ED}${TARGETDIR}/lib/classes/ext/Pure.jar" \
-               "${ED}${TARGETDIR}/lib/classes/ext/scala-library.jar" \
-               "${ED}${TARGETDIR}/lib/classes/ext/scala-swing.jar" \
-               "${ED}${TARGETDIR}/lib/classes/java_ext_dirs.jar"
-}
-
-pkg_postinst() {
-       elog "You will need to re-emerge Isabelle after emerging polyml."
-       elog "Please configure your preferred pdf viewer by editing"
-       elog "the PDF_VIEWER variable in the system settings file"
-       elog "/etc/isabelle/settings and/or the user settings file"
-       elog "\$HOME/.isabelle/${MY_P}/etc/settings"
-}

diff --git a/sci-mathematics/isabelle/isabelle-2012-r1.ebuild 
b/sci-mathematics/isabelle/isabelle-2012-r1.ebuild
deleted file mode 100644
index 087bb7e..0000000
--- a/sci-mathematics/isabelle/isabelle-2012-r1.ebuild
+++ /dev/null
@@ -1,320 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="5"
-
-inherit eutils java-pkg-2 multilib versionator
-
-MY_PN="Isabelle"
-MY_PV=$(replace_all_version_separators '-')
-MY_P="${MY_PN}${MY_PV}"
-
-JEDIT_PV="20120414"
-JEDIT_PN="jedit_build"
-JEDIT_P="${JEDIT_PN}-${JEDIT_PV}"
-
-DESCRIPTION="Isabelle is a generic proof assistant"
-HOMEPAGE="http://www.cl.cam.ac.uk/research/hvg/isabelle/index.html";
-SRC_URI="http://www.cl.cam.ac.uk/research/hvg/isabelle/dist/${MY_P}.tar.gz
-               doc? ( 
https://dev.gentoo.org/~gienah/snapshots/${MY_P}-doc-src.tar.gz )
-               pide? ( http://www4.in.tum.de/~wenzelm/test/${JEDIT_P}.tar.gz )"
-
-LICENSE="BSD"
-SLOT="0/${PV}"
-KEYWORDS="~amd64 ~x86"
-ALL_LOGICS="Pure FOL +HOL ZF CCL CTT Cube FOLP LCF Sequents"
-IUSE="${ALL_LOGICS} doc graphbrowsing ledit readline pide +proofgeneral test"
-
-#upstream says
-#bash 2.x/3.x, Poly/ML 5.x, Perl 5.x,
-#for document preparation: complete LaTeX
-DEPEND=">=app-shells/bash-3.0:*
-               >=dev-lang/polyml-5.4.1:=[-portable]
-               >=dev-lang/perl-5.8.8-r2"
-
-RDEPEND="dev-perl/libwww-perl
-       sci-mathematics/sha1-polyml
-       doc? (
-               virtual/latex-base
-               dev-tex/rail
-       )
-       proofgeneral? (
-               app-emacs/proofgeneral
-       )
-       pide? (
-               >=dev-lang/scala-2.8.2
-       )
-       ledit? (
-               app-misc/ledit
-       )
-       readline? (
-               app-misc/rlwrap
-       )
-       ${DEPEND}"
-
-S="${WORKDIR}"/Isabelle${MY_PV}
-JEDIT_S="${WORKDIR}/${JEDIT_P}"
-TARGETDIR="/usr/share/Isabelle"${MY_PV}
-LIBDIR="/usr/"$(get_libdir)"/Isabelle"${MY_PV}
-
-pkg_setup() {
-       java-pkg-2_pkg_setup
-       if ! use proofgeneral
-       then
-               ewarn "You have deselected the Proof General interface."
-               ewarn "Only a text terminal will be installed."
-               ewarn "Emerge Isabelle with the proofgeneral USE flag enabled"
-               ewarn "to get the common interface, that most people want."
-       fi
-}
-
-src_prepare() {
-       java-pkg-2_src_prepare
-       epatch "${FILESDIR}/${PN}-2012-gentoo-settings.patch"
-       # 
http://article.gmane.org/gmane.science.mathematics.logic.isabelle.devel/2732
-       epatch "${FILESDIR}/${PN}-2012-signal-handling.patch"
-       # 
http://article.gmane.org/gmane.science.mathematics.logic.isabelle.devel/2780
-       epatch 
"${FILESDIR}/${PN}-2012-redundant-equations-in-function-definitions-error.patch"
-       polymlver=$(poly -v | cut -d' ' -f2)
-       polymlarch=$(poly -v | cut -d' ' -f9 | cut -d'-' -f1)
-       sed -e "s@5.4.0@${polymlver}@g" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure polyml version in etc/settings"
-       sed -e "s@ML_HOME=\"/@ML_HOME=\"${ROOT}@" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure polyml ML_HOME in etc/settings"
-       sed -e "s@x86_64@${polymlarch}@g" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure polyml arch in etc/settings"
-       sed -e "s@PROOFGENERAL_HOME=\"/@PROOFGENERAL_HOME=\"${ROOT}@" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure PROOFGENERAL_HOME in etc/settings"
-       sed -e "s@/usr/lib64/Isabelle${MY_PV}@${LIBDIR}@g" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure Isabelle lib directory in 
etc/settings"
-       epatch "${FILESDIR}/${PN}-2012-graphbrowser.patch"
-       epatch "${FILESDIR}/${PN}-2012-libsha1.patch"
-       cat <<- EOF >> "${S}/etc/settings"
-
-               ISABELLE_GHC="${ROOT}usr/bin/ghc"
-               ISABELLE_OCAML="${ROOT}usr/bin/ocaml"
-               ISABELLE_SWIPL="${ROOT}usr/bin/swipl"
-               ISABELLE_JDK_HOME="\$(java-config --jdk-home)"
-               SCALA_HOME="${ROOT}usr/share/scala"
-               SHA1_HOME="/usr/$(get_libdir)/sha1-polyml"
-       EOF
-       if use pide; then
-               cat <<- EOF >> "${S}/etc/settings"
-                       ISABELLE_JEDIT_BUILD_HOME="\$ISABELLE_HOME/${JEDIT_P}"
-                       init_component ${JEDIT_S}
-               EOF
-       fi
-       if use ledit && ! use readline; then
-               epatch "${FILESDIR}/${PN}-2012-reverse-line-editor-order.patch"
-       fi
-}
-
-src_compile() {
-       LOGICS=""
-       for l in "${ALL_LOGICS}"; do
-               if has "${l/+/}"; then
-                       LOGICS="${LOGICS} ${l/+/}"
-               fi
-       done
-       einfo "Building Isabelle logics ${LOGICS}. This may take some time."
-       ./build -b -i "${LOGICS}" || die "building logics failed"
-       ./bin/isabelle makeall || die "isabelle makeall failed"
-       if use graphbrowsing
-       then
-               rm -f "${S}/lib/browser/GraphBrowser.jar" \
-                       || die "failed cleaning graph browser directory"
-               pushd "${S}/lib/browser" \
-                       || die "Could not change directory to lib/browser"
-               ./build || die "failed building the graph browser"
-               popd
-       fi
-       if use pide; then
-               pushd "${S}/src/Tools/jEdit" \
-                       || die "Could not change directory to src/Tools/jEdit"
-               "${S}"/bin/isabelle jedit -b -f \
-                       || die "pide build failed"
-               popd
-               # The jedit_build stuff is only required to build
-               # Isabelle/jEdit Prover IDE (PIDE).  These 2 lines need to be 
deleted
-               # from etc/settings as the jedit_build source code is not 
installed
-               sed -e '/ISABELLE_JEDIT_BUILD_HOME/d' \
-                       -e '/init_component/d' \
-                       -i "${S}/etc/settings" \
-                       || die "Could not delete jedit_build lines from 
etc/settings"
-       fi
-}
-
-src_test() {
-       einfo "Running tests. A test run can take up to several hours!"
-       ./build -b -t || die "tests failed"
-}
-
-src_install() {
-       exeinto ${TARGETDIR}/bin
-       doexe bin/isabelle-process bin/isabelle
-
-       insinto ${TARGETDIR}
-       doins -r src
-       doins -r lib
-
-       docompress -x /usr/share/doc/${PF}
-       dodoc -r doc
-       if use doc; then
-               dosym /usr/share/doc/${PF}/doc "${TARGETDIR}/doc"
-               # The build of sci-mathematics/haskabelle with use doc requires
-               # sci-mathematics/isabelle[doc?]. The haskabelle doc build 
requires
-               # the doc-src directory stuff in the isabelle package.  Which 
is not
-               # provided in the Isabelle 2012 src tarball.  So extract it 
from a
-               # snapshot of the isabelle repo taken soon after the Isabelle 
2012
-               # release.
-               doins -r doc-src
-               for i in "./doc-src/IsarRef/showsymbols" \
-                       "./doc-src/TutorialI/Overview/LNCS/makeDemo" \
-                       "./doc-src/TutorialI/isa-index" \
-                       "./doc-src/sedindex"
-               do
-                       exeinto $(dirname "${TARGETDIR}/${i}")
-                       doexe ${i}
-               done
-       fi
-
-       for i in "./build" \
-               "./src/Pure/mk" \
-               "./src/Pure/build-jars" \
-               "./src/Tools/JVM/build" \
-               "./src/Tools/JVM/java_ext_dirs" \
-               "./src/Tools/jEdit/lib/Tools/jedit" \
-               "./src/Tools/Metis/fix_metis_license" \
-               "./src/Tools/Metis/make_metis" \
-               "./src/Tools/Metis/scripts/mlpp" \
-               "./src/Tools/WWW_Find/lib/Tools/wwwfind" \
-               "./src/Tools/Code/lib/Tools/codegen" \
-               "./src/HOL/Mirabelle/lib/Tools/mirabelle" \
-               "./src/HOL/Tools/Predicate_Compile/lib/scripts/swipl_version" \
-               "./src/HOL/Tools/SMT/lib/scripts/remote_smt" \
-               "./src/HOL/Tools/ATP/scripts/remote_atp" \
-               "./src/HOL/Tools/ATP/scripts/spass" \
-               "./src/HOL/Mutabelle/lib/Tools/mutabelle" \
-               "./src/HOL/TPTP/TPTP_Parser/make_mlyacclib" \
-               "./src/HOL/TPTP/TPTP_Parser/make_tptp_parser" \
-               "./src/HOL/TPTP/lib/Tools/tptp_isabelle_demo" \
-               "./src/HOL/TPTP/lib/Tools/tptp_graph" \
-               "./src/HOL/TPTP/lib/Tools/tptp_isabelle_comp" \
-               "./src/HOL/TPTP/lib/Tools/tptp_refute" \
-               "./src/HOL/TPTP/lib/Tools/tptp_translate" \
-               "./src/HOL/TPTP/lib/Tools/tptp_sledgehammer" \
-               "./src/HOL/TPTP/lib/Tools/tptp_nitpick" \
-               "./src/HOL/Library/Sum_of_Squares/neos_csdp_client" \
-               "./src/HOL/IMP/export.sh" \
-               "./lib/browser/build" \
-               "./lib/Tools/tty" \
-               "./lib/Tools/mkproject" \
-               "./lib/Tools/keywords" \
-               "./lib/Tools/browser" \
-               "./lib/Tools/install" \
-               "./lib/Tools/mkdir" \
-               "./lib/Tools/unsymbolize" \
-               "./lib/Tools/getenv" \
-               "./lib/Tools/java" \
-               "./lib/Tools/make" \
-               "./lib/Tools/emacs" \
-               "./lib/Tools/scala" \
-               "./lib/Tools/print" \
-               "./lib/Tools/latex" \
-               "./lib/Tools/findlogics" \
-               "./lib/Tools/doc" \
-               "./lib/Tools/logo" \
-               "./lib/Tools/usedir" \
-               "./lib/Tools/yxml" \
-               "./lib/Tools/version" \
-               "./lib/Tools/makeall" \
-               "./lib/Tools/scalac" \
-               "./lib/Tools/document" \
-               "./lib/Tools/env" \
-               "./lib/Tools/display" \
-               "./lib/Tools/dimacs2hol" \
-               "./lib/scripts/keywords" \
-               "./lib/scripts/unsymbolize" \
-               "./lib/scripts/run-polyml" \
-               "./lib/scripts/run-smlnj" \
-               "./lib/scripts/feeder" \
-               "./lib/scripts/yxml" \
-               "./lib/scripts/polyml-version" \
-               "./lib/scripts/process"
-       do
-               exeinto $(dirname "${TARGETDIR}/${i}")
-               doexe ${i}
-       done
-
-       dodir /etc/isabelle
-       insinto /etc/isabelle
-       doins -r etc/*
-
-       dosym /etc/isabelle "${TARGETDIR}/etc"
-       dosym "${LIBDIR}/heaps" "${TARGETDIR}/heaps"
-
-       insinto ${LIBDIR}
-       doins -r heaps
-
-       bin/isabelle install -d ${TARGETDIR} -p "${ED}usr/bin" \
-               || die "isabelle install failed"
-       newicon lib/icons/isabelle.xpm "${PN}.xpm"
-       dodoc ANNOUNCE CONTRIBUTORS COPYRIGHT NEWS README
-
-       java-pkg_regjar \
-               "${ED}${TARGETDIR}/src/Tools/JVM/java_ext_dirs.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/QuickNotepad.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/Console.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/ErrorList.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/Hyperlinks.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/SideKick.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/cobra.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/js.jar" \
-               
"${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/scala-compiler.jar" \
-               
"${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/Isabelle-jEdit.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jedit.jar" \
-               "${ED}${TARGETDIR}/lib/classes/ext/scala-swing.jar" \
-               "${ED}${TARGETDIR}/lib/classes/ext/scala-library.jar" \
-               "${ED}${TARGETDIR}/lib/classes/ext/Pure.jar" \
-               "${ED}${TARGETDIR}/lib/browser/GraphBrowser.jar"
-}
-
-pkg_postinst() {
-       # If any of the directories in /etc/isabelle/components do not exist, 
then
-       # even isabelle getenv ISABELLE_HOME fails.  Hence it is necessary to
-       # to delete any non-existing directories.  If an old Isabelle version 
was
-       # installed with component ebuilds like sci-mathematics/e, then the
-       # Isabelle version is upgraded, then the contrib directories will not
-       # exist initially, it is necessary to delete them from 
/etc/isabelle/components.
-       # Then these components are rebuilt (creating these directories) using 
the
-       # EAPI=5 subslot depends.
-       for i in $(egrep '^[^#].*$' "${ROOT}etc/isabelle/components")
-       do
-               if [ ! -d /usr/share/Isabelle2012/${i} ]; then
-                       sed -e "\@${i}@d" -i "${ROOT}etc/isabelle/components"
-               fi
-       done
-       if use ledit && use readline; then
-               elog "Both readline and ledit use flags specified.  The default 
setting"
-               elog "if both are installed is to use readline (rlwrap), this 
can be"
-               elog "modfied by editing the ISABELLE_LINE_EDITOR setting in"
-               elog "${ROOT}/etc/isabelle/settings"
-       fi
-       elog "Please ensure you have a pdf viewer installed, for example:"
-       elog "As root: emerge app-text/zathura-pdf-poppler"
-       elog "Please configure your preferred pdf viewer, something like:"
-       elog "As normal user: xdg-mime default zathura.desktop application/pdf"
-       elog "Or alternatively by editing the PDF_VIEWER variable in the system"
-       elog "settings file ${ROOT}etc/isabelle/settings and/or the user"
-       elog "settings file \$HOME/.isabelle/${MY_P}/etc/settings"
-       elog "To improve sledgehammer performance, consider installing:"
-       elog "USE=isabelle emerge sci-mathematics/e sci-mathematics/spass"
-       elog "For nitpick it is necessary to install:"
-       elog "emerge sci-mathematics/kodkodi"
-}

diff --git a/sci-mathematics/isabelle/isabelle-2013-r2.ebuild 
b/sci-mathematics/isabelle/isabelle-2013-r2.ebuild
deleted file mode 100644
index 6b5c7f6..0000000
--- a/sci-mathematics/isabelle/isabelle-2013-r2.ebuild
+++ /dev/null
@@ -1,353 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="5"
-
-inherit eutils java-pkg-2 multilib versionator
-
-MY_PN="Isabelle"
-MY_PV=$(replace_all_version_separators '-')
-MY_P="${MY_PN}${MY_PV}"
-
-JEDIT_PV="20130104"
-JEDIT_PN="jedit_build"
-JEDIT_P="${JEDIT_PN}-${JEDIT_PV}"
-JEDIT_IC_PN="${JEDIT_PN}-isabelle-component"
-JEDIT_IC_P="${JEDIT_IC_PN}-${JEDIT_PV}"
-
-JFREECHART_PV="1.0.14"
-JFREECHART_PN="jfreechart"
-JFREECHART_P="${JFREECHART_PN}-${JFREECHART_PV}"
-JFREECHART_IC_PN="${JFREECHART_PN}-isabelle-component"
-JFREECHART_IC_P="${JFREECHART_IC_PN}-${JFREECHART_PV}"
-
-SS="2.10"
-
-DESCRIPTION="Isabelle is a generic proof assistant"
-HOMEPAGE="http://www.cl.cam.ac.uk/research/hvg/Isabelle/index.html";
-SRC_URI="http://www.cl.cam.ac.uk/research/hvg/Isabelle/dist/${MY_P}.tar.gz
-               http://isabelle.in.tum.de/components/${JEDIT_P}.tar.gz -> 
${JEDIT_IC_P}.tar.gz
-               http://isabelle.in.tum.de/components/${JFREECHART_P}.tar.gz -> 
${JFREECHART_IC_P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0/${PV}"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc graphbrowsing ledit readline proofgeneral"
-
-#upstream says
-#bash 2.x/3.x, Poly/ML 5.x, Perl 5.x,
-#for document preparation: complete LaTeX
-DEPEND=">=app-shells/bash-3.0:*
-       dev-java/ant-core:0
-       >=dev-java/jcommon-1.0.18:1.0
-       >=dev-java/jfreechart-1.0.14:1.0
-       >=dev-java/itext-2.1.5:0
-       dev-java/xml-xmlbeans:1
-       >=dev-lang/ghc-7.6.3
-       >=dev-lang/polyml-5.5.0:=[-portable]
-       >=dev-lang/perl-5.8.8-r2
-       dev-lang/swi-prolog
-       virtual/jdk:1.7
-       doc? (
-               virtual/latex-base
-               dev-tex/rail
-       )
-       >=dev-lang/scala-2.10.2:${SS}
-       ledit? (
-               app-misc/ledit
-       )
-       readline? (
-               app-misc/rlwrap
-       )"
-
-RDEPEND="dev-perl/libwww-perl
-       sci-mathematics/sha1-polyml
-       >=virtual/jre-1.7
-       proofgeneral? (
-               >=app-emacs/proofgeneral-4.1
-       )
-       ${DEPEND}"
-
-S="${WORKDIR}"/Isabelle${MY_PV}
-JEDIT_S="${WORKDIR}/${JEDIT_P}"
-JFREECHART_S="${WORKDIR}/${JFREECHART_P}"
-TARGETDIR="/usr/share/Isabelle"${MY_PV}
-LIBDIR="/usr/"$(get_libdir)"/Isabelle"${MY_PV}
-
-LIBRARY_PKGS="scala-${SS},itext,jcommon-1.0,jfreechart-1.0,xml-xmlbeans-1"
-
-src_unpack() {
-       unpack "${MY_P}.tar.gz"
-       pushd "${S}/contrib" || die
-       unpack ${JEDIT_IC_P}.tar.gz
-       unpack ${JFREECHART_IC_P}.tar.gz
-}
-
-pkg_setup() {
-       java-pkg-2_pkg_setup
-}
-
-src_prepare() {
-       java-pkg-2_src_prepare
-       java-pkg_getjars ${LIBRARY_PKGS}
-       epatch "${FILESDIR}/${PN}-2013-gentoo-settings.patch"
-       epatch "${FILESDIR}/${PN}-2013-classpath.patch"
-       polymlver=$(poly -v | cut -d' ' -f2)
-       polymlarch=$(poly -v | cut -d' ' -f9 | cut -d'-' -f1)
-       sed -e "s@5.5.0@${polymlver}@g" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure polyml version in etc/settings"
-       sed -e "s@ML_HOME=\"/@ML_HOME=\"${ROOT}@" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure polyml ML_HOME in etc/settings"
-       sed -e "s@x86_64@${polymlarch}@g" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure polyml arch in etc/settings"
-       sed -e "s@PROOFGENERAL_HOME=\"/@PROOFGENERAL_HOME=\"${ROOT}@" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure PROOFGENERAL_HOME in etc/settings"
-       sed -e "s@/usr/lib64/Isabelle${MY_PV}@${LIBDIR}@g" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure Isabelle lib directory in 
etc/settings"
-       epatch "${FILESDIR}/${PN}-2012-graphbrowser.patch"
-       epatch "${FILESDIR}/${PN}-2012-libsha1.patch"
-       # this example fails to compile with swi-prolog 6.5.2, so patch it so 
that
-       # Isabelle will build, then reverse the patch so that the user can see 
the
-       # original code.
-       epatch "${FILESDIR}/${PN}-2013-HOL-Predicate_Compile_Examples.patch"
-       cat <<- EOF >> "${S}/etc/settings"
-
-               ISABELLE_GHC="${ROOT}usr/bin/ghc"
-               ISABELLE_OCAML="${ROOT}usr/bin/ocaml"
-               ISABELLE_SWIPL="${ROOT}usr/bin/swipl"
-               ISABELLE_JDK_HOME="\$(java-config --jdk-home)"
-               SCALA_HOME="${ROOT}usr/share/scala-${SS}"
-               SHA1_HOME="/usr/$(get_libdir)/sha1-polyml"
-       EOF
-       cat <<- EOF >> "${S}/etc/components"
-               #bundled components
-               contrib/${JEDIT_P}
-               contrib/${JFREECHART_P}
-       EOF
-       if use ledit && ! use readline; then
-               epatch "${FILESDIR}/${PN}-2012-reverse-line-editor-order.patch"
-       fi
-       rm -f "${S}/contrib/jfreechart-1.0.14/lib/iText-2.1.5.jar" \
-               "${S}/contrib/jfreechart-1.0.14/lib/jfreechart-1.0.14.jar" \
-               "${S}/contrib/jfreechart-1.0.14/lib/jcommon-1.0.18.jar" \
-               "${S}/lib/classes/ext/scala-actors.jar" \
-               "${S}/lib/classes/ext/scala-compiler.jar" \
-               "${S}/lib/classes/ext/scala-library.jar" \
-               "${S}/lib/classes/ext/scala-reflect.jar" \
-               "${S}/lib/classes/ext/scala-swing.jar" \
-               || die "Could not rm bundled jar files supplied by Gentoo"
-}
-
-src_compile() {
-       einfo "Building Isabelle. This may take some time."
-       ./bin/isabelle build -a -b -s -v || die "isabelle build failed"
-       epatch --reverse 
"${FILESDIR}/${PN}-2013-HOL-Predicate_Compile_Examples.patch"
-       if use graphbrowsing
-       then
-               rm -f "${S}/lib/browser/GraphBrowser.jar" \
-                       || die "failed cleaning graph browser directory"
-               pushd "${S}/lib/browser" \
-                       || die "Could not change directory to lib/browser"
-               ./build || die "failed building the graph browser"
-               popd
-       fi
-       ./bin/isabelle jedit -b -f || die "pide build failed"
-}
-
-src_install() {
-       exeinto ${TARGETDIR}/bin
-       doexe bin/isabelle-process bin/isabelle
-
-       insinto ${TARGETDIR}
-       doins -r src
-       doins -r lib
-       doins -r contrib
-       doins ROOTS
-
-       docompress -x /usr/share/doc/${PF}
-       dodoc -r doc
-       if use doc; then
-               dosym /usr/share/doc/${PF}/doc "${TARGETDIR}/doc"
-               # The build of sci-mathematics/haskabelle with use doc requires
-               # sci-mathematics/isabelle[doc?]. The haskabelle doc build 
requires
-               # the src/Doc directory stuff in the isabelle package.
-               doins -r src/Doc
-               for i in "./src/Doc/Classes/document/build" \
-               "./src/Doc/Codegen/document/build" \
-               "./src/Doc/Functions/document/build" \
-               "./src/Doc/HOL/document/build" \
-               "./src/Doc/Intro/document/build" \
-               "./src/Doc/IsarImplementation/document/build" \
-               "./src/Doc/IsarRef/document/build" \
-               "./src/Doc/IsarRef/document/showsymbols" \
-               "./src/Doc/LaTeXsugar/document/build" \
-               "./src/Doc/Locales/document/build" \
-               "./src/Doc/Logics/document/build" \
-               "./src/Doc/Main/document/build" \
-               "./src/Doc/Nitpick/document/build" \
-               "./src/Doc/ProgProve/document/build" \
-               "./src/Doc/Ref/document/build" \
-               "./src/Doc/Sledgehammer/document/build" \
-               "./src/Doc/System/document/build" \
-               "./src/Doc/Tutorial/document/build" \
-               "./src/Doc/Tutorial/document/isa-index" \
-               "./src/Doc/ZF/document/build" \
-               "./src/Doc/fixbookmarks" \
-               "./src/Doc/prepare_document" \
-               "./src/Doc/sedindex"
-               do
-                       exeinto $(dirname "${TARGETDIR}/${i}")
-                       doexe ${i}
-               done
-       fi
-
-       for i in "./Isabelle " \
-               "./bin/isabelle" \
-               "./bin/isabelle-process" \
-               "./lib/Tools/browser" \
-               "./lib/Tools/build" \
-               "./lib/Tools/build_dialog" \
-               "./lib/Tools/components" \
-               "./lib/Tools/dimacs2hol" \
-               "./lib/Tools/display" \
-               "./lib/Tools/doc" \
-               "./lib/Tools/document" \
-               "./lib/Tools/emacs" \
-               "./lib/Tools/env" \
-               "./lib/Tools/findlogics" \
-               "./lib/Tools/getenv" \
-               "./lib/Tools/install" \
-               "./lib/Tools/java" \
-               "./lib/Tools/keywords" \
-               "./lib/Tools/latex" \
-               "./lib/Tools/logo" \
-               "./lib/Tools/make" \
-               "./lib/Tools/mkdir" \
-               "./lib/Tools/mkproject" \
-               "./lib/Tools/mkroot" \
-               "./lib/Tools/options" \
-               "./lib/Tools/print" \
-               "./lib/Tools/scala" \
-               "./lib/Tools/scalac" \
-               "./lib/Tools/tty" \
-               "./lib/Tools/unsymbolize" \
-               "./lib/Tools/usedir" \
-               "./lib/Tools/version" \
-               "./lib/Tools/yxml" \
-               "./lib/browser/build" \
-               "./lib/scripts/feeder" \
-               "./lib/scripts/getsettings" \
-               "./lib/scripts/keywords" \
-               "./lib/scripts/polyml-version" \
-               "./lib/scripts/process" \
-               "./lib/scripts/run-polyml" \
-               "./lib/scripts/run-smlnj" \
-               "./lib/scripts/unsymbolize" \
-               "./lib/scripts/yxml" \
-               "./src/HOL/IMP/export.sh" \
-               "./src/HOL/Library/Sum_of_Squares/neos_csdp_client" \
-               "./src/HOL/Mirabelle/lib/Tools/mirabelle" \
-               "./src/HOL/Mutabelle/lib/Tools/mutabelle" \
-               "./src/HOL/SPARK/Examples/README" \
-               "./src/HOL/TPTP/TPTP_Parser/make_mlyacclib" \
-               "./src/HOL/TPTP/TPTP_Parser/make_tptp_parser" \
-               "./src/HOL/TPTP/lib/Tools/tptp_graph" \
-               "./src/HOL/TPTP/lib/Tools/tptp_isabelle" \
-               "./src/HOL/TPTP/lib/Tools/tptp_isabelle_hot" \
-               "./src/HOL/TPTP/lib/Tools/tptp_nitpick" \
-               "./src/HOL/TPTP/lib/Tools/tptp_refute" \
-               "./src/HOL/TPTP/lib/Tools/tptp_sledgehammer" \
-               "./src/HOL/Tools/ATP/scripts/dummy_atp" \
-               "./src/HOL/Tools/ATP/scripts/remote_atp" \
-               "./src/HOL/Tools/Predicate_Compile/lib/scripts/swipl_version" \
-               "./src/HOL/Tools/SMT/lib/scripts/remote_smt" \
-               "./src/HOL/Tools/Sledgehammer/MaSh/src/compareStats.py" \
-               "./src/HOL/Tools/Sledgehammer/MaSh/src/mash.py" \
-               "./src/Pure/build" \
-               "./src/Pure/build-jars" \
-               "./src/Tools/Code/lib/Tools/codegen" \
-               "./src/Tools/Graphview/lib/Tools/graphview" \
-               "./src/Tools/Metis/fix_metis_license" \
-               "./src/Tools/Metis/make_metis" \
-               "./src/Tools/Metis/scripts/mlpp" \
-               "./src/Tools/WWW_Find/lib/Tools/wwwfind" \
-               "./src/Tools/jEdit/lib/Tools/jedit"
-       do
-               exeinto $(dirname "${TARGETDIR}/${i}")
-               doexe ${i}
-       done
-
-       insinto /etc/isabelle
-       doins -r etc/*
-       dosym /etc/isabelle "${TARGETDIR}/etc"
-
-       dosym "${LIBDIR}/heaps" "${TARGETDIR}/heaps"
-       insinto ${LIBDIR}
-       doins -r heaps
-
-       bin/isabelle install -d ${TARGETDIR} "${ED}usr/bin" \
-               || die "isabelle install failed"
-       newicon lib/icons/isabelle.xpm "${PN}.xpm"
-       dodoc ANNOUNCE CONTRIBUTORS COPYRIGHT NEWS README
-
-       java-pkg_regjar \
-               
"${ED}${TARGETDIR}/contrib/jedit_build-20130104/contrib/Highlight.jar" \
-               
"${ED}${TARGETDIR}/contrib/jedit_build-20130104/contrib/ErrorList.jar" \
-               
"${ED}${TARGETDIR}/contrib/jedit_build-20130104/contrib/Console.jar" \
-               
"${ED}${TARGETDIR}/contrib/jedit_build-20130104/contrib/cobra.jar" \
-               "${ED}${TARGETDIR}/contrib/jedit_build-20130104/contrib/js.jar" 
\
-               
"${ED}${TARGETDIR}/contrib/jedit_build-20130104/contrib/jedit-5.0.0-patched/jedit.jar"
 \
-               
"${ED}${TARGETDIR}/contrib/jedit_build-20130104/contrib/jedit-5.0.0-patched/jars/QuickNotepad.jar"
 \
-               
"${ED}${TARGETDIR}/contrib/jfreechart-1.0.14/jfreechart-1.0.14-demo.jar" \
-               "${ED}${TARGETDIR}/lib/classes/ext/Graphview.jar" \
-               "${ED}${TARGETDIR}/lib/classes/ext/Pure.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/Console.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/ErrorList.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/Highlight.jar" \
-               
"${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/Isabelle-jEdit.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/QuickNotepad.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/SideKick.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/cobra.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/js.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jedit.jar"
-}
-
-pkg_postinst() {
-       # If any of the directories in /etc/isabelle/components do not exist, 
then
-       # even isabelle getenv ISABELLE_HOME fails.  Hence it is necessary to
-       # to delete any non-existing directories.  If an old Isabelle version 
was
-       # installed with component ebuilds like sci-mathematics/e, then the
-       # Isabelle version is upgraded, then the contrib directories will not
-       # exist initially, it is necessary to delete them from 
/etc/isabelle/components.
-       # Then these components are rebuilt (creating these directories) using 
the
-       # EAPI=5 subslot depends.
-       for i in $(egrep '^[^#].*$' "${ROOT}etc/isabelle/components")
-       do
-               if [ ! -d /usr/share/${MY_P}/${i} ]; then
-                       sed -e "\@${i}@d" -i "${ROOT}etc/isabelle/components"
-               fi
-       done
-       if use ledit && use readline; then
-               elog "Both readline and ledit use flags specified.  The default 
setting"
-               elog "if both are installed is to use readline (rlwrap), this 
can be"
-               elog "modfied by editing the ISABELLE_LINE_EDITOR setting in"
-               elog "${ROOT}/etc/isabelle/settings"
-       fi
-       elog "Please ensure you have a pdf viewer installed, for example:"
-       elog "As root: emerge app-text/zathura-pdf-poppler"
-       elog "Please configure your preferred pdf viewer, something like:"
-       elog "As normal user: xdg-mime default zathura.desktop application/pdf"
-       elog "Or alternatively by editing the PDF_VIEWER variable in the system"
-       elog "settings file ${ROOT}etc/isabelle/settings and/or the user"
-       elog "settings file \$HOME/.isabelle/${MY_P}/etc/settings"
-       elog "To improve sledgehammer performance, consider installing:"
-       elog "USE=isabelle emerge sci-mathematics/e sci-mathematics/spass"
-       elog "For nitpick it is necessary to install:"
-       elog "emerge sci-mathematics/kodkodi"
-}

diff --git a/sci-mathematics/isabelle/isabelle-2013.2-r1.ebuild 
b/sci-mathematics/isabelle/isabelle-2013.2-r1.ebuild
deleted file mode 100644
index 601509a..0000000
--- a/sci-mathematics/isabelle/isabelle-2013.2-r1.ebuild
+++ /dev/null
@@ -1,375 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="5"
-
-inherit eutils java-pkg-2 multilib versionator
-
-MY_PN="Isabelle"
-MY_PV=$(replace_all_version_separators '-')
-MY_P="${MY_PN}${MY_PV}"
-
-JEDIT_PV="20131106"
-JEDIT_PN="jedit_build"
-JEDIT_P="${JEDIT_PN}-${JEDIT_PV}"
-JEDIT_IC_PN="${JEDIT_PN}-isabelle-component"
-JEDIT_IC_P="${JEDIT_IC_PN}-${JEDIT_PV}"
-
-JFREECHART_PV="1.0.14-1"
-JFREECHART_PN="jfreechart"
-JFREECHART_P="${JFREECHART_PN}-${JFREECHART_PV}"
-JFREECHART_IC_PN="${JFREECHART_PN}-isabelle-component"
-JFREECHART_IC_P="${JFREECHART_IC_PN}-${JFREECHART_PV}"
-
-POLYML_PV="5.5.1-1"
-POLYML_PN="polyml"
-POLYML_P="${POLYML_PN}-${POLYML_PV}"
-POLYML_IC_PN="${POLYML_PN}-isabelle-component"
-POLYML_IC_P="${POLYML_IC_PN}-${POLYML_PV}"
-
-SS="2.11"
-
-DESCRIPTION="Isabelle is a generic proof assistant"
-HOMEPAGE="http://www.cl.cam.ac.uk/research/hvg/Isabelle/index.html";
-SRC_URI="http://www.cl.cam.ac.uk/users/lcp/archive/${MY_P}.tar.gz
-               http://isabelle.in.tum.de/components/${JEDIT_P}.tar.gz -> 
${JEDIT_IC_P}.tar.gz
-               http://isabelle.in.tum.de/dist/contrib/${JFREECHART_P}.tar.gz 
-> ${JFREECHART_IC_P}.tar.gz
-               https://dev.gentoo.org/~gienah/snapshots/${POLYML_IC_P}.tar.gz";
-
-LICENSE="BSD"
-SLOT="0/${PV}"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc graphbrowsing ledit readline proofgeneral"
-
-#upstream says
-#bash 2.x/3.x, Poly/ML 5.x, Perl 5.x,
-#for document preparation: complete LaTeX
-DEPEND=">=app-shells/bash-3.0:*
-       dev-java/ant-core:0
-       >=dev-java/jcommon-1.0.18:1.0
-       >=dev-java/jfreechart-1.0.14:1.0
-       >=dev-java/itext-2.1.5:0
-       dev-java/xml-xmlbeans:1
-       dev-java/xz-java:0
-       >=dev-lang/ghc-7.6.3
-       >=dev-lang/polyml-5.5.1:=[-portable]
-       >=dev-lang/perl-5.8.8-r2
-       dev-lang/swi-prolog
-       virtual/jdk:1.7
-       doc? (
-               virtual/latex-base
-               dev-tex/rail
-       )
-       >=dev-lang/scala-2.11.1:${SS}
-       ledit? (
-               app-misc/ledit
-       )
-       readline? (
-               app-misc/rlwrap
-       )"
-
-RDEPEND="dev-perl/libwww-perl
-       sci-mathematics/sha1-polyml
-       >=virtual/jre-1.7
-       proofgeneral? (
-               >=app-emacs/proofgeneral-4.1
-       )
-       ${DEPEND}"
-
-S="${WORKDIR}"/Isabelle${MY_PV}
-JEDIT_S="${WORKDIR}/${JEDIT_P}"
-JFREECHART_S="${WORKDIR}/${JFREECHART_P}"
-TARGETDIR="/usr/share/Isabelle"${MY_PV}
-LIBDIR="/usr/"$(get_libdir)"/Isabelle"${MY_PV}
-
-# Notes on QA warnings: * Class files not found via DEPEND in package.env
-# Stuff with $ in the name appear to be spurious:
-# isabelle/Markup_Tree$$anonfun$results$1$1.class
-# 
scala/tools/nsc/backend/jvm/GenJVM$BytecodeGenerator$$anonfun$computeLocalVarsIndex$1.class
-# It wants javafx, I am unsure how to fix this. I test isabelle with the Sun 
JDK:
-# javafx/application/Platform.class               javafx
-# Presumably the user can provide the jEdit plugins if they are necessary:
-# marker/MarkerSetsPlugin.class                   
http://plugins.jedit.org/plugins/?MarkerSets
-# projectviewer/gui/OptionPaneBase.class          
http://plugins.jedit.org/plugins/?ProjectViewer
-
-LIBRARY_PKGS="ant-core,itext,jcommon-1.0,jfreechart-1.0,scala-${SS},xml-xmlbeans-1,xz-java"
-
-src_unpack() {
-       unpack "${MY_P}.tar.gz"
-       pushd "${S}/contrib" || die
-       unpack ${JEDIT_IC_P}.tar.gz
-       unpack ${JFREECHART_IC_P}.tar.gz
-       unpack ${POLYML_IC_P}.tar.gz
-}
-
-pkg_setup() {
-       java-pkg-2_pkg_setup
-}
-
-src_prepare() {
-       java-pkg-2_src_prepare
-       java-pkg_getjars ${LIBRARY_PKGS}
-       epatch "${FILESDIR}/${PN}-2013-gentoo-settings.patch"
-       epatch "${FILESDIR}/${PN}-2013.2-classpath.patch"
-       polymlver=$(poly -v | cut -d' ' -f2)
-       polymlarch=$(poly -v | cut -d' ' -f9 | cut -d'-' -f1)
-       sed -e "s@5.5.0@${polymlver}@g" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure polyml version in etc/settings"
-       sed -e "s@ML_HOME=\"/@ML_HOME=\"${ROOT}@" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure polyml ML_HOME in etc/settings"
-       sed -e "s@x86_64@${polymlarch}@g" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure polyml arch in etc/settings"
-       sed -e "s@PROOFGENERAL_HOME=\"/@PROOFGENERAL_HOME=\"${ROOT}@" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure PROOFGENERAL_HOME in etc/settings"
-       sed -e "s@/usr/lib64/Isabelle${MY_PV}@${LIBDIR}@g" \
-               -i "${S}/etc/settings" \
-               || die "Could not configure Isabelle lib directory in 
etc/settings"
-       epatch "${FILESDIR}/${PN}-2012-graphbrowser.patch"
-       epatch "${FILESDIR}/${PN}-2012-libsha1.patch"
-       # this example fails to compile with swi-prolog 6.5.2, so patch it so 
that
-       # Isabelle will build, then reverse the patch so that the user can see 
the
-       # original code.
-       epatch "${FILESDIR}/${PN}-2013.2-HOL-Predicate_Compile_Examples.patch"
-       cat <<- EOF >> "${S}/etc/settings"
-
-               ISABELLE_GHC="${ROOT}usr/bin/ghc"
-               ISABELLE_OCAML="${ROOT}usr/bin/ocaml"
-               ISABELLE_SWIPL="${ROOT}usr/bin/swipl"
-               ISABELLE_JDK_HOME="\$(java-config --jdk-home)"
-               SCALA_HOME="${ROOT}usr/share/scala-${SS}"
-               SHA1_HOME="/usr/$(get_libdir)/sha1-polyml"
-       EOF
-       cat <<- EOF >> "${S}/etc/components"
-               #bundled components
-               contrib/${JEDIT_P}
-               contrib/${JFREECHART_P}
-               contrib/${POLYML_P}
-       EOF
-       if use ledit && ! use readline; then
-               epatch "${FILESDIR}/${PN}-2012-reverse-line-editor-order.patch"
-       fi
-       rm -f "${S}/contrib/jfreechart-1.0.14-1/lib/iText-2.1.5.jar" \
-               "${S}/contrib/jfreechart-1.0.14-1/lib/jfreechart-1.0.14.jar" \
-               "${S}/contrib/jfreechart-1.0.14-1/lib/jcommon-1.0.18.jar" \
-               "${S}/lib/classes/ext/scala-actors.jar" \
-               "${S}/lib/classes/ext/scala-compiler.jar" \
-               "${S}/lib/classes/ext/scala-library.jar" \
-               "${S}/lib/classes/ext/scala-reflect.jar" \
-               "${S}/lib/classes/ext/scala-swing.jar" \
-               || die "Could not rm bundled jar files supplied by Gentoo"
-}
-
-src_compile() {
-       einfo "Building Isabelle. This may take some time."
-       ./bin/isabelle build -a -b -s -v || die "isabelle build failed"
-       epatch --reverse 
"${FILESDIR}/${PN}-2013.2-HOL-Predicate_Compile_Examples.patch"
-       if use graphbrowsing
-       then
-               rm -f "${S}/lib/browser/GraphBrowser.jar" \
-                       || die "failed cleaning graph browser directory"
-               pushd "${S}/lib/browser" \
-                       || die "Could not change directory to lib/browser"
-               ./build || die "failed building the graph browser"
-               popd
-       fi
-       ./bin/isabelle jedit -b -f || die "pide build failed"
-}
-
-src_install() {
-       insinto ${TARGETDIR}
-       doins -r src
-       doins -r lib
-       doins -r contrib
-       doins ROOTS
-
-       docompress -x /usr/share/doc/${PF}
-       dodoc -r doc
-       if use doc; then
-               dosym /usr/share/doc/${PF}/doc "${TARGETDIR}/doc"
-               # The build of sci-mathematics/haskabelle with use doc requires
-               # sci-mathematics/isabelle[doc?]. The haskabelle doc build 
requires
-               # the src/Doc directory stuff in the isabelle package.
-               doins -r src/Doc
-               for i in "./src/Doc/Classes/document/build" \
-                       "./src/Doc/Codegen/document/build" \
-                       "./src/Doc/Datatypes/document/build" \
-                       "./src/Doc/fixbookmarks" \
-                       "./src/Doc/Functions/document/build" \
-                       "./src/Doc/Intro/document/build" \
-                       "./src/Doc/IsarImplementation/document/build" \
-                       "./src/Doc/IsarRef/document/build" \
-                       "./src/Doc/IsarRef/document/showsymbols" \
-                       "./src/Doc/JEdit/document/build" \
-                       "./src/Doc/LaTeXsugar/document/build" \
-                       "./src/Doc/Locales/document/build" \
-                       "./src/Doc/Logics/document/build" \
-                       "./src/Doc/Main/document/build" \
-                       "./src/Doc/Nitpick/document/build" \
-                       "./src/Doc/prepare_document" \
-                       "./src/Doc/ProgProve/document/build" \
-                       "./src/Doc/sedindex" \
-                       "./src/Doc/Sledgehammer/document/build" \
-                       "./src/Doc/System/document/build" \
-                       "./src/Doc/Tutorial/document/build" \
-                       "./src/Doc/Tutorial/document/isa-index" \
-                       "./src/Doc/ZF/document/build"
-               do
-                       exeinto $(dirname "${TARGETDIR}/${i}")
-                       doexe ${i}
-               done
-       fi
-
-       for i in "./bin/isabelle" \
-               "./bin/isabelle-process" \
-               "./bin/isabelle_scala_script" \
-               "./lib/browser/build" \
-               "./lib/scripts/feeder" \
-               "./lib/scripts/getsettings" \
-               "./lib/scripts/polyml-version" \
-               "./lib/scripts/process" \
-               "./lib/scripts/run-polyml" \
-               "./lib/scripts/run-polyml-5.5.1" \
-               "./lib/scripts/run-smlnj" \
-               "./lib/scripts/unsymbolize" \
-               "./lib/scripts/update_sub_sup" \
-               "./lib/scripts/yxml" \
-               "./lib/Tools/browser" \
-               "./lib/Tools/build" \
-               "./lib/Tools/components" \
-               "./lib/Tools/display" \
-               "./lib/Tools/doc" \
-               "./lib/Tools/document" \
-               "./lib/Tools/emacs" \
-               "./lib/Tools/env" \
-               "./lib/Tools/findlogics" \
-               "./lib/Tools/getenv" \
-               "./lib/Tools/install" \
-               "./lib/Tools/java" \
-               "./lib/Tools/keywords" \
-               "./lib/Tools/latex" \
-               "./lib/Tools/logo" \
-               "./lib/Tools/mkroot" \
-               "./lib/Tools/options" \
-               "./lib/Tools/scala" \
-               "./lib/Tools/scalac" \
-               "./lib/Tools/tty" \
-               "./lib/Tools/unsymbolize" \
-               "./lib/Tools/update_sub_sup" \
-               "./lib/Tools/version" \
-               "./lib/Tools/yxml" \
-               "./src/HOL/IMP/export.sh" \
-               "./src/HOL/Library/Sum_of_Squares/neos_csdp_client" \
-               "./src/HOL/Mirabelle/lib/Tools/mirabelle" \
-               "./src/HOL/Mutabelle/lib/Tools/mutabelle" \
-               "./src/HOL/SPARK/Examples/README" \
-               "./src/HOL/Tools/ATP/scripts/dummy_atp" \
-               "./src/HOL/Tools/ATP/scripts/remote_atp" \
-               "./src/HOL/Tools/Sledgehammer/MaSh/src/compareStats.py" \
-               "./src/HOL/Tools/Sledgehammer/MaSh/src/mash.py" \
-               "./src/HOL/Tools/Sledgehammer/MaSh/src/server.py" \
-               "./src/HOL/Tools/SMT/lib/scripts/remote_smt" \
-               "./src/HOL/TPTP/lib/Tools/tptp_graph" \
-               "./src/HOL/TPTP/lib/Tools/tptp_isabelle" \
-               "./src/HOL/TPTP/lib/Tools/tptp_isabelle_hot" \
-               "./src/HOL/TPTP/lib/Tools/tptp_nitpick" \
-               "./src/HOL/TPTP/lib/Tools/tptp_refute" \
-               "./src/HOL/TPTP/lib/Tools/tptp_sledgehammer" \
-               "./src/HOL/TPTP/TPTP_Parser/make_mlyacclib" \
-               "./src/HOL/TPTP/TPTP_Parser/make_tptp_parser" \
-               "./src/Pure/build" \
-               "./src/Pure/build-jars" \
-               "./src/Tools/Code/lib/Tools/codegen" \
-               "./src/Tools/Graphview/lib/Tools/graphview" \
-               "./src/Tools/jEdit/lib/Tools/jedit" \
-               "./src/Tools/Metis/fix_metis_license" \
-               "./src/Tools/Metis/make_metis" \
-               "./src/Tools/Metis/scripts/mlpp" \
-               "./src/Tools/WWW_Find/lib/Tools/wwwfind"
-       do
-               exeinto $(dirname "${TARGETDIR}/${i}")
-               doexe ${i}
-       done
-
-       insinto /etc/isabelle
-       doins -r etc/*
-       dosym /etc/isabelle "${TARGETDIR}/etc"
-
-       dosym "${LIBDIR}/heaps" "${TARGETDIR}/heaps"
-       insinto ${LIBDIR}
-       doins -r heaps
-
-       bin/isabelle install -d ${TARGETDIR} "${ED}usr/bin" \
-               || die "isabelle install failed"
-       newicon lib/icons/"${PN}.xpm" "${PN}.xpm"
-       newicon lib/icons/"${PN}-mini.xpm" "${PN}-mini.xpm"
-       dodoc ANNOUNCE CONTRIBUTORS COPYRIGHT NEWS README
-
-       java-pkg_regjar \
-               "${ED}${TARGETDIR}/contrib/${JEDIT_P}/contrib/Console.jar" \
-               "${ED}${TARGETDIR}/contrib/${JEDIT_P}/contrib/ErrorList.jar" \
-               "${ED}${TARGETDIR}/contrib/${JEDIT_P}/contrib/Highlight.jar" \
-               "${ED}${TARGETDIR}/contrib/${JEDIT_P}/contrib/idea-icons.jar" \
-               
"${ED}${TARGETDIR}/contrib/${JEDIT_P}/contrib/jedit-5.1.0-patched/jars/QuickNotepad.jar"
 \
-               
"${ED}${TARGETDIR}/contrib/${JEDIT_P}/contrib/jedit-5.1.0-patched/jedit.jar" \
-               "${ED}${TARGETDIR}/contrib/${JEDIT_P}/contrib/jsr305-2.0.0.jar" 
\
-               "${ED}${TARGETDIR}/contrib/${JEDIT_P}/contrib/MacOSX.jar" \
-               "${ED}${TARGETDIR}/contrib/${JEDIT_P}/contrib/SideKick.jar" \
-               
"${ED}${TARGETDIR}/contrib/${JFREECHART_P}/jfreechart-1.0.14-demo.jar" \
-               "${ED}${TARGETDIR}/lib/browser/GraphBrowser.jar" \
-               "${ED}${TARGETDIR}/lib/classes/Graphview.jar" \
-               "${ED}${TARGETDIR}/lib/classes/Pure.jar" \
-               "${ED}${TARGETDIR}/lib/classes/scala-actors.jar" \
-               "${ED}${TARGETDIR}/lib/classes/scala-compiler.jar" \
-               "${ED}${TARGETDIR}/lib/classes/scala-library.jar" \
-               "${ED}${TARGETDIR}/lib/classes/scala-reflect.jar" \
-               "${ED}${TARGETDIR}/lib/classes/scala-swing.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/Console.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/ErrorList.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/Highlight.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/idea-icons.jar" \
-               
"${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/Isabelle-jEdit.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/jsr305-2.0.0.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/MacOSX.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/QuickNotepad.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jars/SideKick.jar" \
-               "${ED}${TARGETDIR}/src/Tools/jEdit/dist/jedit.jar"
-}
-
-pkg_postinst() {
-       # If any of the directories in /etc/isabelle/components do not exist, 
then
-       # even isabelle getenv ISABELLE_HOME fails.  Hence it is necessary to
-       # to delete any non-existing directories.  If an old Isabelle version 
was
-       # installed with component ebuilds like sci-mathematics/e, then the
-       # Isabelle version is upgraded, then the contrib directories will not
-       # exist initially, it is necessary to delete them from 
/etc/isabelle/components.
-       # Then these components are rebuilt (creating these directories) using 
the
-       # EAPI=5 subslot depends.
-       for i in $(egrep '^[^#].*$' "${ROOT}etc/isabelle/components")
-       do
-               if [ ! -d /usr/share/${MY_P}/${i} ]; then
-                       sed -e "\@${i}@d" -i "${ROOT}etc/isabelle/components"
-               fi
-       done
-       if use ledit && use readline; then
-               elog "Both readline and ledit use flags specified.  The default 
setting"
-               elog "if both are installed is to use readline (rlwrap), this 
can be"
-               elog "modfied by editing the ISABELLE_LINE_EDITOR setting in"
-               elog "${ROOT}/etc/isabelle/settings"
-       fi
-       elog "Please ensure you have a pdf viewer installed, for example:"
-       elog "As root: emerge app-text/zathura-pdf-poppler"
-       elog "Please configure your preferred pdf viewer, something like:"
-       elog "As normal user: xdg-mime default zathura.desktop application/pdf"
-       elog "Or alternatively by editing the PDF_VIEWER variable in the system"
-       elog "settings file ${ROOT}etc/isabelle/settings and/or the user"
-       elog "settings file \$HOME/.isabelle/${MY_P}/etc/settings"
-       elog "To improve sledgehammer performance, consider installing:"
-       elog "USE=isabelle emerge sci-mathematics/e sci-mathematics/spass"
-       elog "For nitpick it is necessary to install:"
-       elog "emerge sci-mathematics/kodkodi"
-}

diff --git a/sci-mathematics/isabelle/metadata.xml 
b/sci-mathematics/isabelle/metadata.xml
index b1da3cf..a23d48b 100644
--- a/sci-mathematics/isabelle/metadata.xml
+++ b/sci-mathematics/isabelle/metadata.xml
@@ -18,20 +18,6 @@ correctness of computer hardware or software and proving
 properties of computer languages and protocols.
 </longdescription>
 <use>
-  <flag name="Pure">Pure is the basis for all object-logics.</flag>
-  <flag name="FOL">FOL (Many-sorted First-Order Logic) provides basic
-  classical and intuitionistic first-order logic. It is polymorphic.</flag>
-  <flag name="HOL">(Higher-Order Logic) is a version of classical higher-order
-  logic resembling that of the HOL System.</flag>
-  <flag name="ZF">ZF (Set Theory) offers a formulation of Zermelo-Fraenkel
-  set theory on top of FOL.</flag>
-  <flag name="CCL">CCL (Classical Computational Logic)</flag>
-  <flag name="CTT">CTT (Constructive Type Theory) is an extensional version
-  of Martin-Löf's Type Theory.</flag>
-  <flag name="Cube">Cube (The Lambda Cube)</flag>
-  <flag name="FOLP">FOLP (FOL with Proof Terms)</flag>
-  <flag name="LCF">LCF (Logic of Computable Functions)</flag>
-  <flag name="Sequents">Sequents (first-order, modal and linear logics)</flag>
   <flag name="graphbrowsing">Generate theory browsing information,
   including HTML documents that show a theory's definition, the
   theorems proved in its ML file and the relationship with its
@@ -41,6 +27,5 @@ properties of computer languages and protocols.
   editor</flag> 
   <flag name="proofgeneral">Add support for the
   <pkg>app-emacs/proofgeneral</pkg> proof assistant front end.</flag>
-  <flag name="pide">Build Isabelle/jEdit Prover IDE (PIDE).</flag> 
 </use>
 </pkgmetadata>