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SQL Queries to be used to find path between two points

For the past year I have been working on an Android based
Transit application that runs off a Restful XML based web service
written in PHP.
I have a little trouble properly querying GTFS Data from my MySQL
Database. I have imported the feed files exactly into the Database as
they are in .cvs form (including Field Names).
Does anyone have proper SQL Queries to be used to find path between two points

If that could be done in SQL (non procedural) it would be very interesting. I imagine it would use connect by syntax, or recursive CTEs. But since those aren't suppported by MySQL or SQLite (not sure which one you're asking about), I would go with doing simple queries and doing the processing in Java.

Is it possible to save persistent objects to the file system

I'd like to save persistent objects to the file system using Hibernate without the need for a SQL database.
Is this possible?

Hibernate works on top of JDBC, so all you need is a JDBC driver and a matching Hibernate dialect.
However, JDBC is basically an abstraction of SQL, so whatever you use is going to look, walk and quack like an SQL database - you might as well use one and spare yourself a lot of headaches. Besides, any such solution is going to be comparable in size and complexity to lighweight Java DBs like Derby.
Of course if you don't insist absolutely on using Hibernate, there are many other options.

It appears that it might technically be possible if you use a JDBC plaintext driver; however I haven't seen any opensource ones which provide write access; the one I found on sourceforge is read-only.

You already have an entity model, I suppose you do not want to lose this nor the relationships contained within it. An entity model is directed to be translated to a relational database.
Hibernate and any other JPA provider (EclipseLink) translate this entity model to SQL. They use a JDBC driver to provide a connection to an SQL database. This, you need to keep as well.
The correct question to ask is: does anybody know an embedded Java SQL database, one that you can start from within Java? There are plenty of those, mentioned in this topic:
HyperSQL: stores the result in an SQL clear-text file, readily imported into any other database
H2: uses binary files, low JAR file size
Derby: uses binary files
Ashpool: stores data in an XML-structured file
I have used HyperSQL on one project for small data, and Apache Derby for a project with huge databases (2Gb and more). Apache Derby performs better on these huge databases.

I don't know exactaly your need, but maybe it's one of below:
1 - If your need is just run away from SQL, you can use a NoSQL database.
Hibernate suports it through Hibernate OGM ( http://www.hibernate.org/subprojects/ogm ).
There are some DBs like Cassandra, MongoDB, CouchDB, Hadoop... You have some suggestions Here
.
2 - Now, if you want not to use a database server (with a service process running always), you can use Apache Derby. It's a DB just like any other SQL, but no need of a server. It uses a singular file to keep data. You can easily transport all database with your program.
Take a look: http://db.apache.org/derby/
3 - If you really want some text plain file, you can do like Michael Borgwardt said. But I don't know if Hibernate would be a good idea in this case.

Both H2 and HyperSQL support embedded mode (running inside your JVM instead of in a separate server) and saving to local file(s); these are still SQL databases, but with Hibernate there's not many other options.

Well, since the question is still opened and the OP said he's opened to new approaches/suggestions, here's mine (a little late but ok).
Do you know Prevayler? It's a Java Prevalence implementation which keep all of your business objects in RAM and mantain Snapshots/Changelogs in the File System, this way it's extremely fast and reliable, since if there's any crash, it'll restore it's last state and reapply every change to it.
Also, it's really easy to setup and run in your app.

Ofcourse this is possible, You can simply use file io features of Java, following steps are required:-
Create a File Object
2.Create an object of FileInputStream (though there are ways which use other Classes)
Wrap this object in a Buffer object or simply inside a java.util.Scanner.
use specific write functions of the object created in previous step.
Note that your object must implement Serializable interface. See following link,

Benefits or using XML over MySQL and vice-versa?

I am currently working on a project that was not made by me but it makes use of a lot XML files instead of MySQL in place of it.
Because of that it makes me wonder if there is really any benefits of using XML over MySQL here.
The scene is, the XML files are loaded only ONCE and used on the server for N things it does.
The XML is only reload if the admin issue a command to the server to reload it.
All the XML files together have an average of maximum 100 mb size.
If you could as well give me a little brief of the above in regards the usage of XML over MySQL would appreciate.
What should I consider to know when a XML would be a better option over a simple innodb or myisam table ?

If your data is read-only and brought into memory only at the command of the admin, then I don't think it's much of an advantage for either technology.
MySQL would have the advantage of SQL queries if you have to search the data. Even in that case it's the type of data that matters. If you have long reference chains/object graphs, then a relational database may be slow because of all the JOINs.
But XML has its own issues. You can easily parse it into a DOM object, but then you only have XPath to search it.

XML is used as one of the ways of storing data. one of using xml is, it makes the data easy to be readable. you can use mysql if there are lot of users need the access to the data at the same time and mysql also supports transactional processing of data whereas xml does not have such features.

just adding the option in between - you could also use some form of xml database like
eXist (http://exist-db.org/index.html) or sedna (http://modis.ispras.ru/sedna/)

XML stored at local storage, and readable only by local server (don't argue me you can use memcache, replicated via rsync or so)
No doubt you can open the XML via a http server, but it will be slow.
While, mysql support port communication, and replication, it basically don't have boundaries if you expanding to multiple servers.
And even at 5.1, mysql support XML

easy object persistence strategy - hibernate?

I'm doing a Java software-project at my university that mainly is about storing data-sets (management of software tests).
The first thing I thought of was a simple SQL DB, however the necessary DB scheme is not available for now (let's say the project is stupid but there's no choice).
Is a persistency framework like Hibernate able to store data internally (for example in XML) and to convert this XML into decent SQL later?
My intention is to use the additional abstraction layer of a framework like Hibernate to save work, because it might have conversion functions. I know that Hibernate can generate class files from SQL, but I'm not too sure whether it needs a DB at every point during development. Using a XML Scheme for now and converting it into SQL later maybe an idea :)

You can persist XML with hibernate into a relational DB, but you cannot use XML directly as a storage engine. Why not simply store you're data into a relational db from the start - you'll create some schema yourself and you'll adapt it to the actual one when you receive it.

I would recommand using a lightweight DB such as HSQLDB instead.

Integrating Pentaho/Talend/etc. with an OR Mapper

We have an application (Java) with an own OR mapper. Within this system we have what can be compared to Hibernate's interceptors (we call it triggers): Do specific actions just before saving data in the database, after it's deleted and so on. The underlying database is MySQL.
Now we would like to use tools such as Pentaho Data Integration or Talend to convert data to put it into our system. It's no problem to do that directly on the SQL level, but by doing so we loose the built-in power of our triggers.
Is there a way to somehow integrate any of the Data Integration solutions into our existing application? It would be great if there was a way to write into instances of our classes instead of writing into the database directly.
Any hints welcome :-)

I'd prefer Talend which is a Java code generator tool. (You can se my blog post at http://www.robertomarchetto.com/www/talend_studio_vs_kettle_pentao_pdi_comparison)
You could use a tJavaRow so you can write Java code for each processed row. In tJavaRow you can call Hibernate code, for example using a custom class defined in a new routine.

2 ways with Pentaho data integration I can think of straight off:
Simply create a plugin which adds/deletes data - you could copy the existing salesforce insert/update plugins, they would be a good start - rip out all the salesforce code and replace with yours.
Perhaps harder; But maybe more satisfying - Write a jdbc driver which uses your code!