Incomplete installation instructions

[jar398]

Incomplete installation instructions

[blackrim]

I am looking into this. I don't quite understand what is going on though (I have been using treemachine pretty extensively the last few days and haven't had the problem).

[blackrim]

I change the language of the readme to be a little more clear. I will be adding more examples to the wiki shortly. Also, could you post the output you are getting so I can try and replicate.

[jar398]

Here's the shell transcript... you asked for it... the key line is 'ls target'

I did disobey one instruction, which was to use maven 2; I used maven 3. Could that be it?

jar@norbert:~/NESCent/opentree-treemachine> sh mvn_cmdline.sh
[INFO] Scanning for projects...
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-assembly-plugin/2.2-beta-5/maven-assembly-plugin-2.2-beta-5.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-assembly-plugin/2.2-beta-5/maven-assembly-plugin-2.2-beta-5.pom (15 KB at 69.5 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-plugins/16/maven-plugins-16.pom
13/13 KB Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-plugins/16/maven-plugins-16.pom (13 KB at 421.5 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/15/maven-parent-15.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/15/maven-parent-15.pom (24 KB at 669.7 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/apache/6/apache-6.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/apache/6/apache-6.pom (13 KB at 430.9 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-assembly-plugin/2.2-beta-5/maven-assembly-plugin-2.2-beta-5.jar
204/204 KB Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-assembly-plugin/2.2-beta-5/maven-assembly-plugin-2.2-beta-5.jar (204 KB at 2999.5 KB/sec)
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building treemachine 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-clean-plugin/2.4.1/maven-clean-plugin-2.4.1.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-clean-plugin/2.4.1/maven-clean-plugin-2.4.1.pom (5 KB at 150.4 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-plugins/18/maven-plugins-18.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-plugins/18/maven-plugins-18.pom (13 KB at 529.0 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/16/maven-parent-16.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/16/maven-parent-16.pom (23 KB at 811.7 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/apache/7/apache-7.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/apache/7/apache-7.pom (15 KB at 469.7 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-clean-plugin/2.4.1/maven-clean-plugin-2.4.1.jar
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-clean-plugin/2.4.1/maven-clean-plugin-2.4.1.jar (23 KB at 821.3 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/2.5/maven-resources-plugin-2.5.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/2.5/maven-resources-plugin-2.5.pom (7 KB at 257.3 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-plugins/19/maven-plugins-19.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-plugins/19/maven-plugins-19.pom (11 KB at 413.4 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/19/maven-parent-19.pom
25/25 KB Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/19/maven-parent-19.pom (25 KB at 842.1 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/apache/9/apache-9.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/apache/9/apache-9.pom (15 KB at 616.9 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/2.5/maven-resources-plugin-2.5.jar
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/2.5/maven-resources-plugin-2.5.jar (26 KB at 946.4 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-compiler-plugin/2.5/maven-compiler-plugin-2.5.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-compiler-plugin/2.5/maven-compiler-plugin-2.5.pom (7 KB at 269.1 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-plugins/22/maven-plugins-22.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-plugins/22/maven-plugins-22.pom (13 KB at 289.4 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/21/maven-parent-21.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/21/maven-parent-21.pom (26 KB at 357.5 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/apache/10/apache-10.pom
15/15 KB Downloaded: http://repo.maven.apache.org/maven2/org/apache/apache/10/apache-10.pom (15 KB at 401.4 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-compiler-plugin/2.5/maven-compiler-plugin-2.5.jar
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-compiler-plugin/2.5/maven-compiler-plugin-2.5.jar (32 KB at 1120.6 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j/1.8.M05/neo4j-1.8.M05.pom
13/13 KB Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/neo4j/1.8.M05/neo4j-1.8.M05.pom (13 KB at 60.9 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/build/parent-central/35/parent-central-35.pom
Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/build/parent-central/35/parent-central-35.pom (10 KB at 191.8 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/build/grandparent/35/grandparent-35.pom
Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/build/grandparent/35/grandparent-35.pom (32 KB at 834.3 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/sonatype/oss/oss-parent/7/oss-parent-7.pom
Downloaded: http://repo.maven.apache.org/maven2/org/sonatype/oss/oss-parent/7/oss-parent-7.pom (5 KB at 196.3 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-kernel/1.8.M05/neo4j-kernel-1.8.M05.pom
14/14 KB Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-kernel/1.8.M05/neo4j-kernel-1.8.M05.pom (14 KB at 60.9 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/geronimo/specs/geronimo-jta_1.1_spec/1.1.1/geronimo-jta_1.1_spec-1.1.1.pom
3/3 KB Downloaded: http://repo.maven.apache.org/maven2/org/apache/geronimo/specs/geronimo-jta_1.1_spec/1.1.1/geronimo-jta_1.1_spec-1.1.1.pom (3 KB at 60.6 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/geronimo/specs/specs/1.4/specs-1.4.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/geronimo/specs/specs/1.4/specs-1.4.pom (12 KB at 316.7 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/geronimo/genesis/config/project-config/1.2/project-config-1.2.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/geronimo/genesis/config/project-config/1.2/project-config-1.2.pom (22 KB at 788.2 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/geronimo/genesis/config/config/1.2/config-1.2.pom
2/2 KB Downloaded: http://repo.maven.apache.org/maven2/org/apache/geronimo/genesis/config/config/1.2/config-1.2.pom (2 KB at 49.6 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/geronimo/genesis/genesis/1.2/genesis-1.2.pom
11/11 KB Downloaded: http://repo.maven.apache.org/maven2/org/apache/geronimo/genesis/genesis/1.2/genesis-1.2.pom (11 KB at 65.7 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/apache/3/apache-3.pom
4/4 KB Downloaded: http://repo.maven.apache.org/maven2/org/apache/apache/3/apache-3.pom (4 KB at 67.0 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-lucene-index/1.8.M05/neo4j-lucene-index-1.8.M05.pom
4/6 KB 6/6 KB Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-lucene-index/1.8.M05/neo4j-lucene-index-1.8.M05.pom (6 KB at 26.4 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/lucene/lucene-core/3.5.0/lucene-core-3.5.0.pom
5/5 KB Downloaded: http://repo.maven.apache.org/maven2/org/apache/lucene/lucene-core/3.5.0/lucene-core-3.5.0.pom (5 KB at 110.9 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/lucene/lucene-parent/3.5.0/lucene-parent-3.5.0.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/lucene/lucene-parent/3.5.0/lucene-parent-3.5.0.pom (2 KB at 43.9 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/lucene/lucene-solr-grandparent/3.5.0/lucene-solr-grandparent-3.5.0.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/lucene/lucene-solr-grandparent/3.5.0/lucene-solr-grandparent-3.5.0.pom (29 KB at 708.0 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-graph-algo/1.8.M05/neo4j-graph-algo-1.8.M05.pom
3/4 KB 4/4 KB Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-graph-algo/1.8.M05/neo4j-graph-algo-1.8.M05.pom (4 KB at 14.3 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-udc/1.8.M05/neo4j-udc-1.8.M05.pom
Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-udc/1.8.M05/neo4j-udc-1.8.M05.pom (7 KB at 26.8 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-graph-matching/1.8.M05/neo4j-graph-matching-1.8.M05.pom
4/4 KB Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-graph-matching/1.8.M05/neo4j-graph-matching-1.8.M05.pom (4 KB at 19.0 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-cypher/1.8.M05/neo4j-cypher-1.8.M05.pom
Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-cypher/1.8.M05/neo4j-cypher-1.8.M05.pom (7 KB at 28.1 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/scala-lang/scala-library/2.9.1-1/scala-library-2.9.1-1.pom
2/2 KB Downloaded: http://repo.maven.apache.org/maven2/org/scala-lang/scala-library/2.9.1-1/scala-library-2.9.1-1.pom (2 KB at 9.5 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-jmx/1.8.M05/neo4j-jmx-1.8.M05.pom
Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-jmx/1.8.M05/neo4j-jmx-1.8.M05.pom (4 KB at 10.3 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/server-api/1.8.M05/server-api-1.8.M05.pom
4/5 KB 5/5 KB Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/server-api/1.8.M05/server-api-1.8.M05.pom (5 KB at 20.3 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/3rdparty/javax/ws/rs/jsr311-api/1.1.2.r612/jsr311-api-1.1.2.r612.pom
Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/3rdparty/javax/ws/rs/jsr311-api/1.1.2.r612/jsr311-api-1.1.2.r612.pom (11 KB at 64.6 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/commons-configuration/commons-configuration/1.6/commons-configuration-1.6.pom
Downloaded: http://repo.maven.apache.org/maven2/commons-configuration/commons-configuration/1.6/commons-configuration-1.6.pom (14 KB at 406.5 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/commons-collections/commons-collections/3.2.1/commons-collections-3.2.1.pom
Downloaded: http://repo.maven.apache.org/maven2/commons-collections/commons-collections/3.2.1/commons-collections-3.2.1.pom (13 KB at 508.8 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/commons/commons-parent/9/commons-parent-9.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/apache/4/apache-4.pom
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Downloading: http://repo.maven.apache.org/maven2/commons-lang/commons-lang/2.4/commons-lang-2.4.pom
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Downloading: http://repo.maven.apache.org/maven2/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.pom
Downloaded: http://repo.maven.apache.org/maven2/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.pom (18 KB at 437.4 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/commons/commons-parent/5/commons-parent-5.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/commons/commons-parent/5/commons-parent-5.pom (16 KB at 391.6 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/commons-beanutils/commons-beanutils-core/1.8.0/commons-beanutils-core-1.8.0.pom
Downloaded: http://repo.maven.apache.org/maven2/commons-beanutils/commons-beanutils-core/1.8.0/commons-beanutils-core-1.8.0.pom (2 KB at 48.5 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/commons-digester/commons-digester/1.8.1/commons-digester-1.8.1.pom
Downloaded: http://repo.maven.apache.org/maven2/commons-digester/commons-digester/1.8.1/commons-digester-1.8.1.pom (10 KB at 349.7 KB/sec)
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Downloading: http://repo.maven.apache.org/maven2/commons-beanutils/commons-beanutils/1.8.0/commons-beanutils-1.8.0.pom
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Downloading: http://repo.maven.apache.org/maven2/log4j/log4j/1.2.17/log4j-1.2.17.pom
Downloaded: http://repo.maven.apache.org/maven2/log4j/log4j/1.2.17/log4j-1.2.17.pom (22 KB at 786.5 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/junit/junit/4.8.1/junit-4.8.1.pom
949/949 B Downloaded: http://repo.maven.apache.org/maven2/junit/junit/4.8.1/junit-4.8.1.pom (949 B at 22.1 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/commons-collections/commons-collections/3.0/commons-collections-3.0.pom
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Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j/1.8.M05/neo4j-1.8.M05.jar
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-lucene-index/1.8.M05/neo4j-lucene-index-1.8.M05.jar
Downloading: http://repo.maven.apache.org/maven2/org/apache/lucene/lucene-core/3.5.0/lucene-core-3.5.0.jar
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-kernel/1.8.M05/neo4j-kernel-1.8.M05.jar
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-graph-algo/1.8.M05/neo4j-graph-algo-1.8.M05.jar
Downloaded: http://repo.maven.apache.org/maven2/org/apache/lucene/lucene-core/3.5.0/lucene-core-3.5.0.jar (1432 KB at 9359.0 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-udc/1.8.M05/neo4j-udc-1.8.M05.jar
Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/neo4j/1.8.M05/neo4j-1.8.M05.jar (23 KB at 106.3 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-graph-matching/1.8.M05/neo4j-graph-matching-1.8.M05.jar
Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-graph-algo/1.8.M05/neo4j-graph-algo-1.8.M05.jar (152 KB at 534.9 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-cypher/1.8.M05/neo4j-cypher-1.8.M05.jar
Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-lucene-index/1.8.M05/neo4j-lucene-index-1.8.M05.jar (152 KB at 402.9 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/scala-lang/scala-library/2.9.1-1/scala-library-2.9.1-1.jar
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Downloading: http://repo.maven.apache.org/maven2/org/neo4j/neo4j-jmx/1.8.M05/neo4j-jmx-1.8.M05.jar
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Downloading: http://repo.maven.apache.org/maven2/org/neo4j/server-api/1.8.M05/server-api-1.8.M05.jar
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Downloading: http://repo.maven.apache.org/maven2/org/neo4j/3rdparty/javax/ws/rs/jsr311-api/1.1.2.r612/jsr311-api-1.1.2.r612.jar
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Downloading: http://repo.maven.apache.org/maven2/commons-configuration/commons-configuration/1.6/commons-configuration-1.6.jar
Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/3rdparty/javax/ws/rs/jsr311-api/1.1.2.r612/jsr311-api-1.1.2.r612.jar (47 KB at 233.9 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/commons-lang/commons-lang/2.4/commons-lang-2.4.jar
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Downloading: http://repo.maven.apache.org/maven2/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar
Downloaded: http://repo.maven.apache.org/maven2/org/neo4j/server-api/1.8.M05/server-api-1.8.M05.jar (117 KB at 240.1 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/commons-beanutils/commons-beanutils-core/1.8.0/commons-beanutils-core-1.8.0.jar
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Downloading: http://repo.maven.apache.org/maven2/commons-digester/commons-digester/1.8.1/commons-digester-1.8.1.jar
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Downloading: http://repo.maven.apache.org/maven2/commons-beanutils/commons-beanutils/1.8.0/commons-beanutils-1.8.0.jar
Downloaded: http://repo.maven.apache.org/maven2/commons-beanutils/commons-beanutils-core/1.8.0/commons-beanutils-core-1.8.0.jar (202 KB at 1934.7 KB/sec)
3117/8640 KB 226/226 KB 2159/3145 KB Downloading: http://repo.maven.apache.org/maven2/log4j/log4j/1.2.17/log4j-1.2.17.jar
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Downloading: http://repo.maven.apache.org/maven2/org/apache/geronimo/specs/geronimo-jta_1.1_spec/1.1.1/geronimo-jta_1.1_spec-1.1.1.jar
Downloaded: http://repo.maven.apache.org/maven2/commons-digester/commons-digester/1.8.1/commons-digester-1.8.1.jar (143 KB at 495.4 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/commons-collections/commons-collections/3.0/commons-collections-3.0.jar
Downloaded: http://repo.maven.apache.org/maven2/org/apache/geronimo/specs/geronimo-jta_1.1_spec/1.1.1/geronimo-jta_1.1_spec-1.1.1.jar (16 KB at 118.6 KB/sec)
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[INFO]
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ treemachine ---
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-api/2.0.6/maven-plugin-api-2.0.6.pom
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/2.0.5/plexus-utils-2.0.5.pom
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Downloaded: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/2.0.5/plexus-utils-2.0.5.jar (218 KB at 7515.2 KB/sec)
[INFO]
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ treemachine ---
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-project/2.0.6/maven-project-2.0.6.pom
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.4.1/plexus-utils-1.4.1.pom
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-container-default/1.0-alpha-9-stable-1/plexus-container-default-1.0-alpha-9-stable-1.pom
Downloaded: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-container-default/1.0-alpha-9-stable-1/plexus-container-default-1.0-alpha-9-stable-1.pom (4 KB at 167.7 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-containers/1.0.3/plexus-containers-1.0.3.pom
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Downloading: http://repo.maven.apache.org/maven2/junit/junit/3.8.1/junit-3.8.1.pom
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.0.4/plexus-utils-1.0.4.pom
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Downloading: http://repo.maven.apache.org/maven2/classworlds/classworlds/1.1-alpha-2/classworlds-1.1-alpha-2.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-profile/2.0.6/maven-profile-2.0.6.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact-manager/2.0.6/maven-artifact-manager-2.0.6.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-parameter-documenter/2.0.6/maven-plugin-parameter-documenter-2.0.6.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/reporting/maven-reporting-api/2.0.6/maven-reporting-api-2.0.6.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/reporting/maven-reporting/2.0.6/maven-reporting-2.0.6.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia-sink-api/1.0-alpha-7/doxia-sink-api-1.0-alpha-7.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia/1.0-alpha-7/doxia-1.0-alpha-7.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-error-diagnostics/2.0.6/maven-error-diagnostics-2.0.6.pom
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Downloading: http://repo.maven.apache.org/maven2/commons-cli/commons-cli/1.0/commons-cli-1.0.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-descriptor/2.0.6/maven-plugin-descriptor-2.0.6.pom
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interactivity-api/1.0-alpha-4/plexus-interactivity-api-1.0-alpha-4.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-monitor/2.0.6/maven-monitor-2.0.6.pom
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Downloading: http://repo.maven.apache.org/maven2/classworlds/classworlds/1.1/classworlds-1.1.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-filtering/1.0/maven-filtering-1.0.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-components/16/maven-shared-components-16.pom
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.5.15/plexus-utils-1.5.15.pom
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus/2.0.2/plexus-2.0.2.pom
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interpolation/1.12/plexus-interpolation-1.12.pom
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-components/1.1.14/plexus-components-1.1.14.pom
Downloaded: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-components/1.1.14/plexus-components-1.1.14.pom (6 KB at 248.0 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/sonatype/plexus/plexus-build-api/0.0.4/plexus-build-api-0.0.4.pom
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Downloading: http://repo.maven.apache.org/maven2/org/sonatype/spice/spice-parent/10/spice-parent-10.pom
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Downloading: http://repo.maven.apache.org/maven2/org/sonatype/forge/forge-parent/3/forge-parent-3.pom
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.5.8/plexus-utils-1.5.8.pom
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interpolation/1.13/plexus-interpolation-1.13.pom
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-components/1.1.15/plexus-components-1.1.15.pom
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus/2.0.3/plexus-2.0.3.pom
Downloaded: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus/2.0.3/plexus-2.0.3.pom (16 KB at 629.1 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/reporting/maven-reporting-api/2.0.6/maven-reporting-api-2.0.6.jar
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia-sink-api/1.0-alpha-7/doxia-sink-api-1.0-alpha-7.jar
Downloading: http://repo.maven.apache.org/maven2/commons-cli/commons-cli/1.0/commons-cli-1.0.jar
Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interactivity-api/1.0-alpha-4/plexus-interactivity-api-1.0-alpha-4.jar
Downloading: http://repo.maven.apache.org/maven2/junit/junit/3.8.1/junit-3.8.1.jar
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/reporting/maven-reporting-api/2.0.6/maven-reporting-api-2.0.6.jar (10 KB at 294.2 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-filtering/1.0/maven-filtering-1.0.jar
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Downloading: http://repo.maven.apache.org/maven2/org/sonatype/plexus/plexus-build-api/0.0.4/plexus-build-api-0.0.4.jar
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interpolation/1.13/plexus-interpolation-1.13.jar
Downloaded: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interactivity-api/1.0-alpha-4/plexus-interactivity-api-1.0-alpha-4.jar (14 KB at 396.8 KB/sec)
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[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 4 resources
[INFO]
[INFO] --- maven-compiler-plugin:2.5:compile (default-compile) @ treemachine ---
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-api/2.0.9/maven-plugin-api-2.0.9.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven/2.0.9/maven-2.0.9.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/8/maven-parent-8.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0.9/maven-artifact-2.0.9.pom
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.5.1/plexus-utils-1.5.1.pom
Downloaded: http://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.5.1/plexus-utils-1.5.1.pom (3 KB at 97.5 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-core/2.0.9/maven-core-2.0.9.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-settings/2.0.9/maven-settings-2.0.9.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/maven-settings/2.0.9/maven-settings-2.0.9.pom (3 KB at 91.4 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-model/2.0.9/maven-model-2.0.9.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-parameter-documenter/2.0.9/maven-plugin-parameter-documenter-2.0.9.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-profile/2.0.9/maven-profile-2.0.9.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/maven-profile/2.0.9/maven-profile-2.0.9.pom (3 KB at 74.1 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/2.0.9/maven-repository-metadata-2.0.9.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-error-diagnostics/2.0.9/maven-error-diagnostics-2.0.9.pom
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-project/2.0.9/maven-project-2.0.9.pom
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/maven-project/2.0.9/maven-project-2.0.9.pom (3 KB at 115.1 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact-manager/2.0.9/maven-artifact-manager-2.0.9.pom
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[INFO] Compiling 26 source files to /dsk/jar/NESCent/opentree-treemachine/target/classes
[INFO]
[INFO] --- maven-assembly-plugin:2.2-beta-5:single (default-cli) @ treemachine ---
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[jar398]

Looks like the transcript got truncated. I've deposited the entire transcript here:

https://gist.github.com/jar398/4715296

[blackrim]

OK, looks like the problem is that you should build EITHER the standalone or the server plugins. So when you do both, the server plugins cleans the previous files to make sure there are no conflicts. if you just do sh mvn_cmdline.sh then you will see the jar. I can make that clear in the README.md