Bump isabelle to 2013.2. Fix Bug 536324 - sci-mathematics/isabelle: Slot dependencies for java packages. Add upper range dependency <dev-lang/scala-2.11.1 to 2013-r1.

Package-Manager: portage-2.2.15/cvs/Linux x86_64
Manifest-Sign-Key: 0x618E971F

6 files changed, 629 insertions, 19 deletions

diff --git a/sci-mathematics/isabelle/ChangeLog b/sci-mathematics/isabelle/ChangeLog
index 26d53a1136be..0a19e8e72d60 100644
--- a/sci-mathematics/isabelle/ChangeLog
+++ b/sci-mathematics/isabelle/ChangeLog
@@ -1,6 +1,16 @@
 # ChangeLog for sci-mathematics/isabelle
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/isabelle/ChangeLog,v 1.11 2014/01/07 13:36:33 tomwij Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/isabelle/ChangeLog,v 1.12 2015/01/25 13:08:28 gienah Exp $
+
+*isabelle-2013.2 (25 Jan 2015)
+
+  25 Jan 2015; Mark Wright <gienah@gentoo.org>
+  +files/isabelle-2013.2-HOL-Predicate_Compile_Examples.patch,
+  +files/isabelle-2013.2-classpath.patch, +isabelle-2013.2.ebuild,
+  isabelle-2013-r1.ebuild:
+  Bump isabelle to 2013.2. Fix Bug 536324 - sci-mathematics/isabelle: Slot
+  dependencies for java packages. Add upper range dependency <dev-
+  lang/scala-2.11.1 to 2013-r1.
 
 *isabelle-2012-r1 (07 Jan 2014)
 *isabelle-2013-r1 (07 Jan 2014)
diff --git a/sci-mathematics/isabelle/Manifest b/sci-mathematics/isabelle/Manifest
index b0ee31d37b0a..b394fe2d8c6a 100644
--- a/sci-mathematics/isabelle/Manifest
+++ b/sci-mathematics/isabelle/Manifest
@@ -15,27 +15,30 @@ AUX isabelle-2012-signal-handling.patch 457 SHA256 df6e274300a8ac440fa140c7bdb13
 AUX isabelle-2013-HOL-Predicate_Compile_Examples.patch 3388 SHA256 690917da79d2c4db7055dbabcff0923a604674ac3b82616e596aeb128034b7fd SHA512 105b7067a9e9470ee8f54212cb8ec4ff50806a9c3b2468eae7972884267c27da33c0606850376f7d318f40dcddbc0305235f895c1409d88412d917c9c973fc0a WHIRLPOOL 7bbe4d3e254ea1b677189daf9bd7925e497dfd386df7466d2e81bd6e11ba46dfa8bcb3cd8b662baf479f8e0e58eb2f3feea6eecf54d88c064adba803a9f85893
 AUX isabelle-2013-classpath.patch 5309 SHA256 5b6fad7851876fd1e070e12b714688aad749f7e85d83665aa99abb5a74ad9233 SHA512 47874fd4570ffa865cca1069f2e5189d0765ecac0df65e19997ea50f6ebe2790ed9b588a3d4669c9abca4c67b3c160d4cf563171b20218c8729391cb82f2b197 WHIRLPOOL 3d6e8d8e87ff11ceae025cae987f7901f765b64f01e5fd7cbf7c06715b8758e9648c8066adc01ce91920aaf1526108db80f008b818ce85dbbb938888a45f521e
 AUX isabelle-2013-gentoo-settings.patch 600 SHA256 8b8a0bd49fa4bc58222906c6d0315b03a09144b5c419acb21c03bad4ee13cdfb SHA512 d9eee090f79f5d4a82cb478160f69ac107ba486925ca1e87ea3cfbc84c402155665b384803b9b78c52514568d90ba77a177abfdf004a4ca9c4080eb49879b0e2 WHIRLPOOL 2b132ae5c8a57b440ec11a70a25061251d1bfb6551627848df21bce907a10834f7889d277a3f5c6cb9928817142c8aa1f08be2b8b783f84c766a6c5309d79863
+AUX isabelle-2013.2-HOL-Predicate_Compile_Examples.patch 3365 SHA256 f6eb29e06d2411bd74d68a987972ab975d35e28004404761b920f61cb9a7a43d SHA512 a2302959545ce7ac4783c8f076bded4fe98695c0fda17b5c0c015ac2a43a5daa92d11081ef8f33aa03a6db2b8770955b284ea04cc06d7f5d3ccec2c497598665 WHIRLPOOL ec5bdf3878b60f64875dff645c441907674d59e23845308f97951f2f06ca36c7af9eede75c1d310011231b9ef963f99fa225418f72d7a90c39d3b0f24fe74cf4
+AUX isabelle-2013.2-classpath.patch 4404 SHA256 425f1481799367627c5bea0915eb7609331a4028d17ec538d8eb74f7fe073db0 SHA512 b665a26d5e09d35eceb0b770dfbf5a67a715e91d29f8b9d06813035c0ed74c2501fc158522ca133b4de66468042859360b5754c2518f67f03e42efa11608179c WHIRLPOOL fb4eff34fc8ad8d36fd28fd8e7b9cc0f7361af66360e19148c99ceb6bfabf72026ca100e59ba20e59d3293b766e821720d2b8e86ba8e4ce459183f7d65ca7644
 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
 EBUILD isabelle-2011.1-r2.ebuild 8115 SHA256 1425dc7fc5b6fb1410acc5c2eb09f48ee470e8fe23f3c330021cda8d813ebb9a SHA512 e6d4cf8c1971086a1fb2ac786b4e48eb38ceb1a00932e8df91bcbb9e743ce641170ab73f2d9c175f4901b862a376c3a1a685c09e8e3ea46371558406ce0c1b20 WHIRLPOOL a3f91037261b947da149bc600c9a3b7c7b9ed7c5f2c2e4f7811cecbb5c47967ae7a9fde667d29db6452e5390901fe26c4a9b89f2341fe8228ce0d9d3d88b32e0
 EBUILD isabelle-2011.1.ebuild 4036 SHA256 6063b32c39e50c42e81051197ce46a735bb16448c13b5ff1f8af5018f07b3020 SHA512 430524175bd5fbf4beb325a93ef746bf5df5c2beabc4b6d9536c1f7370e0c1babdd9bf00a617076a74ff892e5909ffe01f791a7121bdf3fb3cd817eb42f4bf66 WHIRLPOOL 3e3bcc27aa6ff8f4853fb142c0a4312bb7eeb908639a3fc826ae882a16fca60c03374387f4e06b19f4b079afb562d782d786c75c1c4a36c2cac2db47c0f04e18
 EBUILD isabelle-2012-r1.ebuild 11015 SHA256 1e15911e89af34332811e04a25c84c7730338a7b17a295b59ac71fa9515b9fd4 SHA512 725559331033b7b7a7e7fb68fe7cce89adc44e7cbd9cc3f3e0b28810bd667417def64b26ec803b5bb51065a34c10d0dad31fed2f0e7e38b41b352fddeda885da WHIRLPOOL 18aeb75c4e68e4470aa2793924c615f951534e03ee7dc8bf347084727d32f1b1037dfdedbf8cff849edd35ab7bf97b08fe73c5519b283bd97f9e4077b799af8d
-EBUILD isabelle-2013-r1.ebuild 12422 SHA256 ff89eb0b63eb62ba526c6494c4f918ce998061fe11ff35470afb742e62313e49 SHA512 ae6e923f20e245b7de54d08629b1b11b3127123e43abc54d61f82169c0e6a64f2b20eddba40984948beb3bd10aaae0f083a5b67d2dfc10d24c35bc4eaa1acf81 WHIRLPOOL d60571fb1c02ee26566d60db1feae1f029c6539dadae85342eeb95fbeb6a84d9cf00c7ee23cfae114797021af60f8ddec64bc82017d1e3a7075f9d3e6be0d607
-MISC ChangeLog 3660 SHA256 d4e9cb022d8a2e5fcd95d190e863303a7aeb0e5c60ab19519fff1293344200e2 SHA512 e9b7af18f18ebaa5502396ecbec1bebab737d7ef919b05d41f468e1ea6fae048a63a1e4defbaf3416f6eeb4e69c939fc900e4fd8e9e8186c290c82360a12271a WHIRLPOOL 4f34b0412990de4216f1a0b531d135d0a742db3b4d92bb3c04a4e1f2e3b2cf3c6d4670cf3333d568c478f81fa48759d9ccc9542f7bedf72e960d8cf92ecf2d74
+EBUILD isabelle-2013-r1.ebuild 12457 SHA256 06bfd1a23a8758d2c373088aa63fd7fcfb6ec2c5e6bcc83f8028c00336bac595 SHA512 0f17e9519343c89af699a1cef81662f287ccc10a423f6764d1ef7189a7efc2abe9637671f280ff40b3d3766bea2080a8d81c163fd9e6d8e6538c0f9ba039c47a WHIRLPOOL aead60121b7a2324c49fb6a249cf21a11d3d255b04bf3f8654cfe893c51382099fd0450ccd3aaccee953ba98721e307cb3555062b3c873cff9b6c4db5ce76ac3
+EBUILD isabelle-2013.2.ebuild 13887 SHA256 31e9e7bb4c411dcf8c2b29deeb0f0ea91ccf4fd36887f659c666146e846f3b08 SHA512 c79226870182f1d2c74ecb689636342590cb43bab6293c49e379662c9a926950b911de40909e828ceba38f4201257f7bfa8f535736a75017ae31641a566c28a8 WHIRLPOOL 1891f1852a7441c3a0a9ce7a0849480ec575a7dd868fe450b74de1508160994b606770ac9e08d602c9b2be0bd93236bcb406abbc95324532bea18e83687517eb
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 MISC metadata.xml 2156 SHA256 cade1f090a62a67146e6ebce508a20436e2c883d62dbc5a260733a60f69bd43b SHA512 cade4e370f3adbf9a5ae9bc6a73adabbe36f3ccc707c47f6f4516f2f0604b26f34439cff170bf478b3d52f0c507d72d9eef8f69657d7de2fda1f70a8a96de137 WHIRLPOOL 2edf4ab8a07ba560d34e168a9fd618a6fc1f9946dd0f9b62a2d071d1f19546d5e15413f54658c898e1e71df0c110ea832529f95cf904b7333489734fdfd5749b
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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..4532bd3b8ad3
--- /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	2014-02-09 20:53:30.085279943 +1100
+@@ -10,5 +10,5 @@
+ unset CLASSPATH
+ 
+ isabelle_jdk java "${JAVA_ARGS[@]}" \
+-  -classpath "$(jvmpath "$ISABELLE_CLASSPATH")" "$@"
++  -classpath "$(jvmpath "$ISABELLE_CLASSPATH:$(java-config -p scala | sed 's@\([^:]*\)/[^:]*:.*@\1@')")" "$@"
+ 
+--- Isabelle2013-2-orig/lib/Tools/scala	2013-12-06 02:18:34.000000000 +1100
++++ Isabelle2013-2/lib/Tools/scala	2014-02-09 20:54:22.418737591 +1100
+@@ -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 | sed 's@\([^:]*\)/[^:]*:.*@\1@')")" "$@"
+ 
+--- Isabelle2013-2-orig/lib/Tools/scalac	2013-12-06 02:18:34.000000000 +1100
++++ Isabelle2013-2/lib/Tools/scalac	2014-02-09 20:55:03.999895037 +1100
+@@ -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 | 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-2013-r1.ebuild b/sci-mathematics/isabelle/isabelle-2013-r1.ebuild
index f85f9aec6e48..6f57d1ef679f 100644
--- a/sci-mathematics/isabelle/isabelle-2013-r1.ebuild
+++ b/sci-mathematics/isabelle/isabelle-2013-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/isabelle/isabelle-2013-r1.ebuild,v 1.1 2014/01/07 13:36:33 tomwij Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/isabelle/isabelle-2013-r1.ebuild,v 1.2 2015/01/25 13:08:28 gienah Exp $
 
 EAPI="5"
 
@@ -37,10 +37,10 @@ IUSE="doc graphbrowsing ledit readline proofgeneral"
 #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
-	>=dev-java/jcommon-1.0.18
-	>=dev-java/jfreechart-1.0.14
-	>=dev-java/itext-2.1.5
+	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]
@@ -51,7 +51,7 @@ DEPEND=">=app-shells/bash-3.0
 		virtual/latex-base
 		dev-tex/rail
 	)
-	>=dev-lang/scala-2.10.2
+	>=dev-lang/scala-2.10.2 <dev-lang/scala-2.11.1
 	ledit? (
 		app-misc/ledit
 	)
diff --git a/sci-mathematics/isabelle/isabelle-2013.2.ebuild b/sci-mathematics/isabelle/isabelle-2013.2.ebuild
new file mode 100644
index 000000000000..7e6d8cf25bd1
--- /dev/null
+++ b/sci-mathematics/isabelle/isabelle-2013.2.ebuild
@@ -0,0 +1,373 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/isabelle/isabelle-2013.2.ebuild,v 1.1 2015/01/25 13:08:28 gienah Exp $
+
+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}"
+
+DESCRIPTION="Isabelle is a generic proof assistant"
+HOMEPAGE="http://www.cl.cam.ac.uk/research/hvg/Isabelle/index.html"
+SRC_URI="http://isabelle.in.tum.de/dist/${MY_P}.tar.gz
+		http://isabelle.in.tum.de/components/${JEDIT_P}.tar.gz -> ${JEDIT_IC_P}.tar.gz
+		http://isabelle.in.tum.de/dist/contrib/${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
+	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$1.class
+# It wants javafx, I am unsure how to fix this. I test isabelle with the Sun JDK:
+# javafx/application/Platform.class               javafx
+# Presumably the user can provide the jEdit plugins if they are necessary:
+# marker/MarkerSetsPlugin.class                   http://plugins.jedit.org/plugins/?MarkerSets
+# projectviewer/gui/OptionPaneBase.class          http://plugins.jedit.org/plugins/?ProjectViewer
+
+LIBRARY_PKGS="ant-core,itext,jcommon-1.0,jfreechart-1.0,scala,xml-xmlbeans-1,xz-java"
+
+src_unpack() {
+	unpack "${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="${ROOT}usr/share/scala"
+		SHA1_HOME="/usr/$(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_build-20131106/contrib/Console.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/ErrorList.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/Highlight.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/idea-icons.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/jedit-5.1.0-patched/jars/QuickNotepad.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/jedit-5.1.0-patched/jedit.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/jsr305-2.0.0.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/MacOSX.jar" \
+		"${ED}${TARGETDIR}/contrib/jedit_build-20131106/contrib/SideKick.jar" \
+		"${ED}${TARGETDIR}/contrib/jfreechart-1.0.14-1/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"
+}