Maybe you're referring to `neo4j-shell`, as the suggested commands have no 
effect for me with `neo4j console` (Neo4j 2.3.2 Community, OSX 10.11.3). 
The docs here <http://neo4j.com/docs/stable/re01.html> also state:

console 

Start the server as an application, running as a foreground process. Stop 
the server using CTRL-C.


And with Ctrl-C, shutdown *appears* to be graceful:

$ neo4j console
...

2016-03-06 13:52:33.555-0600 INFO  Remote interface ready and available at 
http://localhost:7474/

quit

^D

^C2016-03-06 13:52:50.748-0600 INFO  Neo4j Server shutdown initiated by 
request

...

2016-03-06 13:52:50.852-0600 INFO  Successfully stopped database

2016-03-06 13:52:50.852-0600 INFO  Successfully shutdown database



On Sunday, March 6, 2016 at 1:25:38 AM UTC-6, Michael Hunger wrote:
>
> Clean shutdown
>
> Ie "quit" or ctrl-d
>
>
>
> Von meinem iPhone gesendet
>
> Am 06.03.2016 um 00:47 schrieb Jesse Hemingway <jiro...@gmail.com 
> <javascript:>>:
>
> Ok, that certainly works. That's a bit boggling -- I have quite a few 
> indexes and constraints, if that could have any effect. I also use the 
> TimeTree module by GraphAware (several at once). I'll play around with a 
> few combinations when I have time to focus on that oddity and hopefully 
> report back with more useful information. Also, when do the disused records 
> get recovered – on shutdown? I'm just running with `neo4j console`, killing 
> it with Ctrl+C each time.
>
> On Sat, Mar 5, 2016 at 3:10 PM, Michael Hunger <
> michael...@neotechnology.com <javascript:>> wrote:
>
>> Interesting, it works for me:
>>
>> on empty db, create 100k nodes 100k rels delete everything, check sizes
>> restart create 100k nodes 100k rels delete everything, check sizes
>> same size on disk 
>>
>> wuqour:neo4j-enterprise-2.3.2 mh$ rm -rf test*.db
>>
>> wuqour:neo4j-enterprise-2.3.2 mh$ bin/neo4j-shell -path test.db
>>
>> NOTE: Local Neo4j graph database service at 'test.db'
>>
>> Welcome to the Neo4j Shell! Enter 'help' for a list of commands
>>
>>
>>
>> neo4j-sh (?)$ foreach(x in range(1,100000) | create (:Person 
>> {name:"person "+x, age : x % 100}));
>>
>> +-------------------+
>>
>> | No data returned. |
>>
>> +-------------------+
>>
>> Nodes created: 100000
>>
>> Properties set: 200000
>>
>> Labels added: 100000
>>
>> 5996 ms
>>
>> neo4j-sh (?)$ unwind range(1,100000) as x match (p) where id(p) = x match 
>> (p2) where id(p2) = toInt(rand()*100000) create (p)-[:KNOWS]->(p2);
>>
>> +-------------------+
>>
>> | No data returned. |
>>
>> +-------------------+
>>
>> Relationships created: 99999
>>
>> 3185 ms
>>
>> neo4j-sh (?)$ match (n) detach delete n;
>>
>> +-------------------+
>>
>> | No data returned. |
>>
>> +-------------------+
>>
>> Nodes deleted: 100000
>>
>> Relationships deleted: 99999
>>
>> 1654 ms
>>
>> neo4j-sh (?)$ quit
>>
>> wuqour:neo4j-enterprise-2.3.2 mh$ du -sh test.db/neostore*.db
>>
>> 8,0K test.db/neostore.labeltokenstore.db
>>
>> 1,4M test.db/neostore.nodestore.db
>>
>> 3,9M test.db/neostore.propertystore.db
>>
>> 8,0K test.db/neostore.relationshipgroupstore.db
>>
>> 3,2M test.db/neostore.relationshipstore.db
>>
>> 8,0K test.db/neostore.relationshiptypestore.db
>>
>> 8,0K test.db/neostore.schemastore.db
>>
>> wuqour:neo4j-enterprise-2.3.2 mh$ bin/neo4j-shell -path test.db
>>
>> NOTE: Local Neo4j graph database service at 'test.db'
>>
>> Welcome to the Neo4j Shell! Enter 'help' for a list of commands
>>
>>
>>
>> neo4j-sh (?)$ foreach(x in range(1,100000) | create (:Person 
>> {name:"person "+x, age : x % 100}));
>>
>> +-------------------+
>>
>> | No data returned. |
>>
>> +-------------------+
>>
>> Nodes created: 100000
>>
>> Properties set: 200000
>>
>> Labels added: 100000
>>
>> 5911 ms
>>
>> neo4j-sh (?)$ unwind range(1,100000) as x match (p) where id(p) = x match 
>> (p2) where id(p2) = toInt(rand()*100000) create (p)-[:KNOWS]->(p2);
>>
>> +-------------------+
>>
>> | No data returned. |
>>
>> +-------------------+
>>
>> Relationships created: 99999
>>
>> 1897 ms
>>
>> neo4j-sh (?)$ match (n) detach delete n;
>>
>> +-------------------+
>>
>> | No data returned. |
>>
>> +-------------------+
>>
>> Nodes deleted: 100000
>>
>> Relationships deleted: 99999
>>
>> 1415 ms
>>
>> neo4j-sh (?)$ wuqour:neo4j-enterprise-2.3.2 mh$ du -sh 
>> test.db/neostore*.db
>>
>> 8,0K test.db/neostore.labeltokenstore.db
>>
>> 1,4M test.db/neostore.nodestore.db
>>
>> 3,9M test.db/neostore.propertystore.db
>>
>> 8,0K test.db/neostore.relationshipgroupstore.db
>>
>> 3,2M test.db/neostore.relationshipstore.db
>>
>> 8,0K test.db/neostore.relationshiptypestore.db
>>
>> 8,0K test.db/neostore.schemastore.db
>>
>> On Sat, Mar 5, 2016 at 6:43 PM, Jesse Hemingway <jiro...@gmail.com 
>> <javascript:>> wrote:
>>
>>> This is not holding true for my setup, as I've seen my modest 10MB 
>>> database grow to 250MB over the course of repeatedly testing my seeding 
>>> logic, and shutting down the server many times as I made configuration 
>>> changes for new modules, etc. Also, this SO article 
>>> <http://stackoverflow.com/questions/24368176/neo4j-empty-database-takes-up-a-lot-of-disk-space>
>>>  
>>> (outdated? but seems to hold true) indicates that space is not reclaimed. 
>>> I've come across a tool in the public domain to accomplish neo4j 
>>> compaction, implying it isn't (or wasn't) automatically supported.
>>>
>>> I repeated the restart-server test just now, and it does not alter the 
>>> size on disk -- the store is 18.2MB (19.4 on disk), twice my 'fresh' data 
>>> size, and I have reset/reseeded once. Next, I deleted the db, and after 
>>> reseeding, the size is back down to 9.14, with all the same data as before. 
>>> My log files were a drop in the bucket either way.
>>>
>>> Either way, I'm not going to quibble that if it's more efficient to 
>>> re-use old records than create new ones, it doesn't make sense to 
>>> aggressively compact the database. It would just be nice as an option, e.g. 
>>> to assist in file transfer when moving a database around, etc.
>>>
>>>
>>> On Saturday, March 5, 2016 at 7:18:56 AM UTC-6, Michael Hunger wrote:
>>>>
>>>> Unused recoreds are reclaimed after restart, so if you restart after 
>>>> cleaning out then it will.
>>>> But you can also just delete the db-directory.
>>>>
>>>> On Fri, Mar 4, 2016 at 10:52 PM, Jesse Hemingway <jiro...@gmail.com> 
>>>> wrote:
>>>>
>>>>> I actually just delete my database if I want to reset everything to a 
>>>>> clean slate (shutting down server first). We have an auto-seeding 
>>>>> solution 
>>>>> that reconstitutes our base data, so that may not be an option for you. 
>>>>> Otherwise, MATCH <stuff> DETACH DELETE <stuff> does the job.
>>>>>
>>>>> But on a related note, I notice that e.g. repeated use of MATCH (n) 
>>>>> DETACH DELETE n (with reseeding in between) does not seem to reclaim 
>>>>> data storage, and the overall database size keeps growing. Is this 
>>>>> expected 
>>>>> behavior, or is there some garbage-collection process I need to trigger?
>>>>>
>>>>>
>>>>> On Saturday, February 27, 2016 at 6:43:52 PM UTC-6, Ara wrote:
>>>>>>
>>>>>> Hi ,
>>>>>>    Recently installed Neo4j community version, I'am not able to clear 
>>>>>> the node labels, relationship type from database information. Kindly 
>>>>>> guide 
>>>>>> me on this issue.Thank you
>>>>>>
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