proj/gentoo: Initial commit

This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
author: Robin H. Johnson <robbat2@gentoo.org> 2015-08-08 13:49:04 -0700
committer: Robin H. Johnson <robbat2@gentoo.org> 2015-08-08 17:38:18 -0700
commit: 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch)
tree: 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-mathematics/isabelle
download: gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz
gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2
gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip
23 files changed, 2223 insertions, 0 deletions
diff --git a/sci-mathematics/isabelle/Manifest b/sci-mathematics/isabelle/Manifest
new file mode 100644
index 000000000000..f3bd2a8ec892
--- /dev/null
+++ b/sci-mathematics/isabelle/Manifest
@@ -0,0 +1,11 @@
+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 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 jfreechart-isabelle-component-1.0.14-1.tar.gz 3444825 SHA256 b0eb7365c4c5877379889100f081a4afc4117afc0d332941c3dd01bef2c4aee9 SHA512 ee1d84a45e43029d5e3acee823176196da19789322e8d3c2c81d5504930ad81d50e16e5da87655e4151034901daefb4ce6b82334839e39134b3a7ce32203aa67 WHIRLPOOL e6f9caadb802ecb5b784e86e96c008e9271aa0b1c940152fb0b0358280d9c1e274bb0dee1507f8ff0fe7f43f863db538d631c76e146d1f66ab6e8a8fb27eb42d
+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 682e25b677e1b0401a43d4cff35c69658359b4c74f86d3459c050e7c7b0d17f1de1e7b792f2a51f97acf574ad56b3e89ade688bc24d090b3e89eaf0cb99a08d5
diff --git a/sci-mathematics/isabelle/files/isabelle-2011.1-gentoo-settings.patch b/sci-mathematics/isabelle/files/isabelle-2011.1-gentoo-settings.patch
new file mode 100644
index 000000000000..67e3476f2170
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2011.1-gentoo-settings.patch
@@ -0,0 +1,39 @@
+--- 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
new file mode 100644
index 000000000000..ed8036a9b2d4
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2011.1-graphbrowser.patch
@@ -0,0 +1,11 @@
+--- 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
new file mode 100644
index 000000000000..905a1eb60e5f
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2011.1-libsha1.patch
@@ -0,0 +1,11 @@
+--- 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
new file mode 100644
index 000000000000..67e3476f2170
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2011.1-proofgeneral-gentoo-path.patch
@@ -0,0 +1,39 @@
+--- 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
new file mode 100644
index 000000000000..b2f2c35ee087
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2011.1-reverse-line-editor-order.patch
@@ -0,0 +1,12 @@
+--- 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
new file mode 100644
index 000000000000..8994491445d5
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2012-gentoo-settings.patch
@@ -0,0 +1,62 @@
+--- 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-graphbrowser.patch b/sci-mathematics/isabelle/files/isabelle-2012-graphbrowser.patch
new file mode 100644
index 000000000000..3e63f1c62237
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2012-graphbrowser.patch
@@ -0,0 +1,11 @@
+--- Isabelle2012-orig/lib/browser/build	2012-05-20 19:34:33.000000000 +1000
++++ Isabelle2012/lib/browser/build	2012-05-26 22:18:41.952750622 +1000
+@@ -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-2012-libsha1.patch b/sci-mathematics/isabelle/files/isabelle-2012-libsha1.patch
new file mode 100644
index 000000000000..06933669de7f
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2012-libsha1.patch
@@ -0,0 +1,11 @@
+--- Isabelle2012-orig/src/Pure/General/sha1_polyml.ML	2012-05-20 19:34:33.000000000 +1000
++++ Isabelle2012/src/Pure/General/sha1_polyml.ML	2012-12-05 23:24:06.263793934 +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-2012-redundant-equations-in-function-definitions-error.patch b/sci-mathematics/isabelle/files/isabelle-2012-redundant-equations-in-function-definitions-error.patch
new file mode 100644
index 000000000000..18ae43d00fe5
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2012-redundant-equations-in-function-definitions-error.patch
@@ -0,0 +1,35 @@
+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-reverse-line-editor-order.patch b/sci-mathematics/isabelle/files/isabelle-2012-reverse-line-editor-order.patch
new file mode 100644
index 000000000000..233ea5b50fad
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2012-reverse-line-editor-order.patch
@@ -0,0 +1,12 @@
+--- Isabelle2012-orig/etc/settings	2012-05-23 03:07:38.000000000 +1000
++++ Isabelle2012/etc/settings	2012-05-27 12:43:36.209715015 +1000
+@@ -62,8 +62,8 @@
+ ###
+ 
+ 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-signal-handling.patch b/sci-mathematics/isabelle/files/isabelle-2012-signal-handling.patch
new file mode 100644
index 000000000000..d238f41bd32b
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2012-signal-handling.patch
@@ -0,0 +1,8 @@
+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
new file mode 100644
index 000000000000..bce7eec4417c
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2013-HOL-Predicate_Compile_Examples.patch
@@ -0,0 +1,82 @@
+--- 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
new file mode 100644
index 000000000000..e3b2271a30c5
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2013-classpath.patch
@@ -0,0 +1,149 @@
+--- 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-gentoo-settings.patch b/sci-mathematics/isabelle/files/isabelle-2013-gentoo-settings.patch
new file mode 100644
index 000000000000..7066c6b875a2
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2013-gentoo-settings.patch
@@ -0,0 +1,19 @@
+--- Isabelle2013-orig/etc/settings	2013-02-13 00:31:02.000000000 +1100
++++ Isabelle2013/etc/settings	2013-08-17 14:47:46.045988000 +1000
+@@ -176,3 +176,16 @@
+ #ISABELLE_GHC="/usr/bin/ghc"
+ #ISABELLE_OCAML="/usr/bin/ocaml"
+ #ISABELLE_SWIPL="/usr/bin/swipl"
++
++# Poly/ML Gentoo (x86_64)
++ML_PLATFORM=x86_64-linux
++ML_HOME="/usr/bin"
++ML_SYSTEM=polyml-5.5.0
++ML_OPTIONS="-H 1000"
++ML_SOURCES="/usr/src/debug/dev-lang/polyml-5.5.0"
++
++# Proof General home
++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-2013.2-HOL-Predicate_Compile_Examples.patch b/sci-mathematics/isabelle/files/isabelle-2013.2-HOL-Predicate_Compile_Examples.patch
new file mode 100644
index 000000000000..e1253016837b
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2013.2-HOL-Predicate_Compile_Examples.patch
@@ -0,0 +1,89 @@
+--- Isabelle2013-2-orig/src/HOL/Predicate_Compile_Examples/Hotel_Example_Prolog.thy	2013-12-06 02:18:50.000000000 +1100
++++ Isabelle2013-2/src/HOL/Predicate_Compile_Examples/Hotel_Example_Prolog.thy	2014-02-09 22:21:20.676081140 +1100
+@@ -87,7 +87,7 @@
+ *}
+ 
+ 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 *}
+@@ -115,7 +115,7 @@
+ 
+ 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 *} 
+@@ -151,7 +151,7 @@
+ 
+ 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
+--- Isabelle2013-2-orig/src/HOL/Predicate_Compile_Examples/Context_Free_Grammar_Example.thy	2013-12-06 02:18:50.000000000 +1100
++++ Isabelle2013-2/src/HOL/Predicate_Compile_Examples/Context_Free_Grammar_Example.thy	2014-02-09 22:27:26.826238011 +1100
+@@ -36,7 +36,7 @@
+ 
+ lemma
+   "S\<^sub>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)"
+@@ -70,7 +70,7 @@
+ 
+ theorem S\<^sub>1_sound:
+ "S\<^sub>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
+ 
+ 
+@@ -94,7 +94,7 @@
+ 
+ theorem S\<^sub>2_sound:
+   "S\<^sub>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\<^sub>3 and A\<^sub>3 and B\<^sub>3 where
+@@ -171,4 +171,4 @@
+ hide_const a b
+ 
+ 
+-end
+\ No newline at end of file
++end
+--- Isabelle2013-2-orig/src/HOL/Predicate_Compile_Examples/Lambda_Example.thy	2013-12-06 02:18:50.000000000 +1100
++++ Isabelle2013-2/src/HOL/Predicate_Compile_Examples/Lambda_Example.thy	2014-02-09 22:21:20.677081168 +1100
+@@ -95,7 +95,7 @@
+ 
+ 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 *}
+--- Isabelle2013-2-orig/src/HOL/Predicate_Compile_Examples/List_Examples.thy	2013-12-06 02:18:50.000000000 +1100
++++ Isabelle2013-2/src/HOL/Predicate_Compile_Examples/List_Examples.thy	2014-02-09 22:21:20.678081196 +1100
+@@ -24,7 +24,7 @@
+ 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-2013.2-classpath.patch b/sci-mathematics/isabelle/files/isabelle-2013.2-classpath.patch
new file mode 100644
index 000000000000..b3ad4ae95cd9
--- /dev/null
+++ b/sci-mathematics/isabelle/files/isabelle-2013.2-classpath.patch
@@ -0,0 +1,135 @@
+--- 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
new file mode 100644
index 000000000000..6b96bcb57260
--- /dev/null
+++ b/sci-mathematics/isabelle/isabelle-2011.1-r2.ebuild
@@ -0,0 +1,254 @@
+# 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
new file mode 100644
index 000000000000..f0e0c82faab2
--- /dev/null
+++ b/sci-mathematics/isabelle/isabelle-2011.1.ebuild
@@ -0,0 +1,142 @@
+# 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
new file mode 100644
index 000000000000..e6afded3e5a1
--- /dev/null
+++ b/sci-mathematics/isabelle/isabelle-2012-r1.ebuild
@@ -0,0 +1,320 @@
+# 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? ( http://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
new file mode 100644
index 000000000000..6b5c7f622f8c
--- /dev/null
+++ b/sci-mathematics/isabelle/isabelle-2013-r2.ebuild
@@ -0,0 +1,353 @@
+# 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
new file mode 100644
index 000000000000..99fabbc9d239
--- /dev/null
+++ b/sci-mathematics/isabelle/isabelle-2013.2-r1.ebuild
@@ -0,0 +1,375 @@
+# 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 -> ${JFREECHART_IC_P}.tar.gz
+		http://dev.gentoo.org/~gienah/snapshots/${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
new file mode 100644
index 000000000000..41285400dc40
--- /dev/null
+++ b/sci-mathematics/isabelle/metadata.xml
@@ -0,0 +1,43 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<maintainer>
+  <email>gienah@gentoo.org</email>
+</maintainer>
+<herd>sci-mathematics</herd>
+<longdescription lang='en'>
+Isabelle is a generic proof assistant. It allows mathematical
+formulas to be expressed in a formal language and provides tools
+for proving those formulas in a logical calculus. The main
+application is the formalization of mathematical proofs and in
+particular formal verification, which includes proving the
+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
+  ancestors and descendants.</flag>
+  <flag name='ledit'>Use ledit for the isabelle tty line editor</flag> 
+  <flag name='readline'>Use readline (rlwrap) for the isabelle tty line
+  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>
author	Robin H. Johnson <robbat2@gentoo.org>	2015-08-08 13:49:04 -0700
committer	Robin H. Johnson <robbat2@gentoo.org>	2015-08-08 17:38:18 -0700
commit	56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch)
tree	3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-mathematics/isabelle
download	gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip