The original poster is using the Community version on Windows, as am I. Despite what anyone has said, no one has actually answered the question with verifiable, tested results. I originally said, "This is not an answer". However, I now tend to think it IS the answer, just not the desired result. The answer is, to the best of my knowledge, with my specific tests and results documented below: NOWHERE: YOU CAN'T CONFIGURE current stable 1.9.4 or milestone 2.0.0-M06 Community versions on Windows x64.
I have tried the suggestions under the best answer, which were untested and unverified, and they do not work. See specific quotations below.
Neither of the currently pushed 2.0.0-M06 or stable 1.9.4 Community versions are configurable in any way, shape or form on Windows -- given the current documentation and non-answers. As a first time user to Neo4j with these two versions, this has been very frustrating, to have no clear way to configure the software, and incorrect official documentation.
"Also: the 2.0 installer is still a traditional configuration, complete with conf folder, where you can make all the configuration changes you need to make." @David Makagon
This is a false statement. It is the same as 1.9.4, no conf folders anywhere on disk.
"I suspect you could place the neo4j-server.properties file into the JAR file here as well (though I haven't tried)." @David Makagon
I have tried both Neo4j Community 1.9.4 and 2.0.0-M06 x64 on Windows 7 x64, running as a user, with and without running as administrator.
I've used ProcMon and could not even find any attempt to read any "conf" file at documented location. However, I found other odd locations with a "config" in the name, and have tried there also, out of morbid curiosity, included below.
Summary of config file locations which DO NOT work:
C:\Program Files\Neo4j Community\conf\neo4j-default.properties [1.9.4]
C:\Program Files\Neo4j Community\conf\neo4j-server.properties [1.9.4, 2.0.0-M06]
C:\Program Files\Neo4j Community\bin\neo4j-community.exe.Config [1.9.4]
C:\Program Files\Neo4j Community\bin\neo4j-default.properties [1.9.4]
C:\Program Files\Neo4j Community\bin\neo4j-server.properties [1.9.4]
C:\Program Files\Neo4j Community\bin\conf\neo4j-server.properties [2.0.0-M06]
C:\Program Files\Neo4j Community\bin\neo4j-desktop-1.9.4.jar\org\neo4j\server\config\community\neo4j-default.properties
C:\Program Files\Neo4j Community\bin\neo4j-desktop-1.9.4.jar\org\neo4j\server\config\community\neo4j-server.properties
C:\Program Files\Neo4j Community\bin\neo4j-desktop-1.9.4\org\neo4j\server\config\community\neo4j-default.properties
C:\Program Files\Neo4j Community\bin\neo4j-desktop-1.9.4\org\neo4j\server\config\community\neo4j-server.properties
C:\Users\root\Documents\Neo4j\neo4j-default.properties [1.9.4]
C:\Users\root\Documents\Neo4j\neo4j-server.properties [1.9.4]
C:\Users\root\Documents\Neo4j\conf\neo4j-default.properties [1.9.4]
C:\Users\root\Documents\Neo4j\conf\neo4j-server.properties [1.9.4]
C:\Users\root\Documents\Neo4j\default.graphdb\neo4j.properties [1.9.4, 2.0.0-M06]
C:\Users\root\Documents\Neo4j\default.graphdb\neo4j-server.properties [1.9.4]
C:\Users\root\Documents\Neo4j\default.graphdb\conf\neo4j-server.properties [1.9.4]
Also note, the jar's config file
C:\Program Files\Neo4j Community\bin\neo4j-desktop-1.9.4.jar\org\neo4j\server\config\community\neo4j-default.properties
corresponds directly to (exact same file, no differences)
C:\Users\root\Documents\Neo4j\default.graphdb\neo4j.properties
Yet changing the port in this location also does nothing.
Is there a way to configure this through the webadmin? It is definitely not clear at all.