Prior to Java 9, I had assumed that packages were a way to promote/enforce modularization of code and to solve the namespacing problem. Packages actually do a really poor problem of solving the latter (com.popkernel.myproject.Employee myEmployee = new com.popkernel.myproject.Employee();, ugh) so I primarily focused on the former benefit.
And while packages do a very poor job at enforcing modularity, I've found them quite effective at promoting modularity. "What package does this class belong in?" has always been an illuminating question, and I appreciate that Java forces me to ask myself it.
But now Java 9 modules are here and they enforce the modularity problem better than packages. In fact, you could compose a new project entirely out of modules where each module wraps a single package.
Of course, modules are a LOT of extra boilerplate compared to packages, not to mention the quirk that unlike packages, it is impossible to tell what module a class belongs to just by examining its .java file.
So going forward my plan for using packages and modules together is: as I'm writing code, group related concepts into packages. Then, if I decide I want to distribute the code I'm working on, formalize it into a module.
Is that a sane way to utilize those concepts in tandem?
Is that a sane way to utilize those concepts in tandem?
Yes, kind of. Though there are other benefits that you can gain from modularising your code such as Reliable configuration, Strong encapsulation, Increased Readability etc.
So going forward my plan for using packages and modules together is:
as I'm writing code, group related concepts into packages. Then, if I
decide I want to distribute the code I'm working on, formalize it into
a module.
A quick question you can ask yourself is that while you would be using modules, and as you would group related concepts into packages, eventually how do you group related packages then?
The answer that could match up to the reason is the introduction of a new kind of Java program component - Modules
A module is a named, self-describing collection of code and data. Its
code is organized as a set of packages containing types, i.e.,
Java classes and interfaces; its data includes resources and other
kinds of static information.
Until now such collections were primarily targeted as JAR files, that were distributed to be consumed as dependencies/libraries within other, but they are becoming legacy formats and differ quite a bit with modules. In one of my recent answers to Java 9 - What is the difference between "Modules" and "JAR" files? I have tried to detail the differences.
I'm new to Java. I've discovered, while trying to structure my code, that Java intimately ties source file organisation (directory structure) to package structure and package structure to external visibility of classes (a class is either visible to all other packages, or none).
This makes it quite difficult to organise the internal implementation details of my public library into logical units of related functionality while maintaining good encapsulation. JSR 294 explains it best:
Today, an implementation can be partitioned into multiple packages.
Subparts of such an implementation need to be more tightly coupled to
each other than to the surrounding software environment. Today
designers are forced to declare elements of the program that are
needed by other subparts of the implementation as public - thereby
making them globally accessible, which is clearly suboptimal.
Alternately, the entire implementation can be placed in a single
package. This resolves the issue above, but is unwieldy, and exposes
all internals of all subparts to each other.
So my question is, what workarounds exist for this limitation, and what are the pros & cons? Two are mentioned in the JSR - use packages for logical grouping (violating encapsulation); place everything in a single package (unwieldy). Are there other pros/cons to these workarounds? Are there other solutions? (I've become vaguely aware of OSGi bundles, but I've found it hard to understand how they work and what the the pros/cons might be (perhaps that's a con). It appears to be very intrusive compared to vanilla packages, to development & deployment.
Note: I'll upvote any good answers, but the the best answer will be one that comprehensively folds in the pros & cons of others (plagiarise!).
Related (but not duplicate!) questions
Anticipating cries of 'Possible duplicate', here are similar questions that I've found on SO; I present them here for reference and also to explain why they don't answer my question.
Java : Expose only a single package in a jar file: asks how to do it, but given that it's not possible in current releases of Java, doesn't discuss workarounds. Has interesting pointers to forthcoming Modularization (Project Jigsaw) in Java 8.
Package and visibility - duplicate question of the above, basically.
Best practice for controlling access to a ".internal" package - question and answers seem to be specific to OSGi or Eclipse plug-ins.
Tools like ProGuard can be used to repackage a JAR, exposing only those classes you specify in the configuration file. (It does this in addition to optimizing, inlining, and obfuscating.) You might be able to set up ProGuard in e.g. a Maven or Ant build, so you write your library exposing methods as public, and then use ProGuard to eliminate them from the generated JAR.
I'll get the ball rolling. Steal this answer and add to it/correct it/elaborate please!
Use multiple packages for multiple logical groupings
Pros: effective logical grouping of related code.
Cons: when internal implementation detail classes in different packages need to use one another, they must be made public - even to the end user - violating encapsulation. (Work around this by using a standard naming convention for packages containing internal implementation details such as .internal or .impl).
Put everything in one package
Pros: effective encapsulation
Cons: unwieldy for development/maintenance of the library if it contains many classes
Use OSGi bundles
Pros: ? (do they fix the problem?)
Cons: appears to be very intrusive at development (for both library user and author) and deployment, compared to just deploying .jar files.
Wait for Jigsaw in Java 8
http://openjdk.java.net/projects/jigsaw/
Pros: fixes the problem for good?
Cons: doesn't exist yet, not specific release date known.
I've never found this to be a problem. The workaround (if you want to call it that) is called good API design.
If you design your library well, then you can almost always do the following:
Put the main public API in one package e.g. "my.package.core" or just "my.package"
Put helper modules in other packages (according to logical groupings), but give each one it's own public API subset (e.g. a factory class like "my.package.foobarimpl.FoobarFactory")
The main public API package uses only the public API of helper modules
Your tests should also run primarily against the public APIs (since this is what you care about in terms of regressions or functionality)
To me the "right level of encapsulation" for a package is therefore to expose enough public API that your package can be used effectively as a dependency. No more and no less. It shouldn't matter whether it is being used by another package in the same library or by an external user. If you design your packages around this principle, you increase the chance of effective re-use.
Making parts of a package "globally accessible" really doesn't do any harm as long as your API is reasonably well designed. Remember that packages aren't object instances and as a result encapsulation doesn't matter nearly as much: making elements of a package public is usually much less harmful than exposing internal implementation details of a class (which I agree should almost always be private/protected).
Consider java.lang.String for example. It has a big public API, but whatever you do with the public API can't interfere with other users of java.lang.String. It's perfectly safe to use as a dependency from multiple places at the same time. On the other hand, all hell would break loose if you allowed users of java.lang.String to directly access the internal character array (which would allow in-place mutation of immutable Strings.... nasty!!).
P.S. Honourable mention goes to OSGi because it is a pretty awesome technology and very useful in many circumstances. However its sweet spot is really around deployment and lifecycle management of modules (stopping / starting / loading etc.). You don't really need it for code organisation IMHO.
As projects that I'm working on grow larger and larger, I'm starting to be pretty unsure about dividing classes into packages. Suppose the project has a lot of layers and in these layers are interfaces and implementation and even more sublayers (components). I always end up with a lot of packages which starts to be little confusing.
So I want to know other people's approaches to working with packages. Do you prefer to have a lot of packages with few classes or few packages with a lot of classes? Do you prefer to separate implementations from interfaces? And so on... In general your daily habits of using packages and pros/cons of your approach.
Thank you for your posts.
Packages are meant to help you find things.
If they make it more confusing than it is, you're not doing something quite right. If the package structure isn't intuitive, it can actually be harder to find classes than in a flat structure.
There are two basic schools of organising classes into packages as far as I know:
Organising by module first. Here your higher level packages are different modules of the system and you might split it further by function.
Organising by function. Here you organise by function first (e.g. all controller classes in one package, all your data containers in another and so on) and optionally subdivide it by module.
There are pros and cons for both systems, I find them roughlty equal, although I prefer the module approach slightly.
The really important thing is though to follow one system and don't mix it with the other. Don't shoehorn classes into packages they don't belong to and don't be afraid to create a new package if your new class doesn't seem to belong to any of your existing ones.
If a package seems to have grown too large, you might want to split it. But the decision of whether a package should be split or not should be made on whether there is a clear conceptual divide between classes therein and not on numbers. A package with a single class is just as good as a package with thirty classes if it's obvious why they're there.
As for separating interfaces and implementations, first off, I'd probably question the need for them. Ever so often I come across interfaces with only one reasonable implementation, which makes me question their reason to exist. (Sometimes there is a good reason, but often there isn't.)
But if you have multiple implementations for a given interface, then yes, I'd separate them. The interface would be com.foo.Bar and the implementations would be something like com.foo.bars.CrowBar, com.foo.bars.TaskBar for example. Obviously, if your implementations belong to different modules, then you would change it to com.foo.moduleX.bars.CrowBar or com.foo.bars.moduleX.CrowBar, depending on which system you're following.
Re-reading all this, it does sound kind of complicated, but probably the first sentence is the most important: don't follow packaging principles blindly, packages should help you find classes, not hinder you.
I prefer to limit the scope of my classes and methods to private or package protected wherever possible (so they don't clutter Eclipse's autocomplete:) which automatically means that packages can contain quite a few classes.
I do prefer to separate business data objects (DAO's) from their repositories/retrieval services, which are separated from business logic objects and views.
Sets of related functionality with no cross dependencies tend to go in their own artifact as I tend to reuse logic. Especially handy when you start playing with OSGi and independent services.
One thing is important, the publicly exported interface (public interfaces, enums and classes) need to be somewhat related so the package documentation shows some cohesion.
I recently looked at a Java application which had a very fine-grained package structure. Many packages only contained one or two classes and many sub packages. Also many packages contained more sub packages than actual classes.
Is this a good or a bad thing?
IMO, it is a bad thing, though not a real show-stopper in terms of maintainability.
The disadvantages are that it makes classes harder to find, and that it makes the package names more verbose. The former applies more when you are not using an IDE.
It could be argued that it helps modularization in conjunction with "package private" scoping. But conversely, you could also argue that over-packagization actually does the opposite; i.e. forcing you to use public where you wouldn't have had to if you'd been less fine-grained / pedantic.
The actual number of types that end up in one particular package is not that important. It is how you arrive at your package structure.
Things like abstraction ("what" instead of "how", essentially "public" API), coupling (the degree of how dependent a package is on other packages) and cohesion (how interrelated is the functionality in one package) are more important.
Some guidelines for package design (mostly from Uncle Bob) are for example:
Packages should form reusable and releasable modules
Packages should be focussed for good reusability
Avoid cyclic dependencies between packages
Packages should depend only on packages that change less often
The abstraction of a package should be in proportion to how often it changes
Do not try to flesh out an entire package structure from scratch (You Are Not Going To Need It). Instead let it evolve and refactor often. Look at the import section of your Java sources for inspiration on moving types around. Don't be distracted by packages that contain only one or a few types.
I think finer grained package structure is a good thing. The main reason is it can help minimize your dependencies. But be careful... if you break things up too much that actually belong together, you will end up with circular dependencies!
As a rule of thumb, I usually have an interface (or group of related interfaces) in a package. And in subpackages I will have implementations of those interfaces (instead of having all the implementations in the same package). That way a client can just depend on the interface and implementation of interest... and not all the other stuff they don't need.
Hope this helps.
It is subjective, of course, but I generally prefer to decide my packages in a way they would contain at least 3-4 classes, but not more than about 13-15. It makes understanding better, while not cluttering the project. For others it might be different, though.
In case a package grows more than 13-15 classes, a subpackage is asking to emerge.
A package is a unit of encapsulation.
Ideally, it exposes a public API via interface(s) and hides implementation detail in package private classes.
The size of the package is therefore the number of classes needed to implement the public API.
There is also the magical number 7 +/- 2. Within physiological circles it has been shown that this is a basic limit on our ability to comprehend a given set of things. How much we can keep in short term memory and process at the same time before our brains need to start swapping. It is not a bad rule of thumb I've found when coding, ie once a package starts getting bigger than 10 classes it is time to think seriously about splitting it up, but below 5 packages it is really not worth it. Also applies well to things like menu organisation. See Millers paper, or google.
When writing from scratch my way is to begin all classes in the root package (com.example.app1). When there is a certain amount of interrelated classes that "do a whole thing" is time to create a package. After some time developing helper classes may go to a generic package (ex. com.example.app1.misc, com.example.app1.utils) to unload the root package.
So i try to keep clean the root package.
Fine-grain is not bad but as other said often refactoring produce a compact package structure.
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I thought about this awhile ago and it recently resurfaced as my shop is doing its first real Java web app.
As an intro, I see two main package naming strategies. (To be clear, I'm not referring to the whole 'domain.company.project' part of this, I'm talking about the package convention beneath that.) Anyway, the package naming conventions that I see are as follows:
Functional: Naming your packages according to their function architecturally rather than their identity according to the business domain. Another term for this might be naming according to 'layer'. So, you'd have a *.ui package and a *.domain package and a *.orm package. Your packages are horizontal slices rather than vertical.
This is much more common than logical naming. In fact, I don't believe I've ever seen or heard of a project that does this. This of course makes me leery (sort of like thinking that you've come up with a solution to an NP problem) as I'm not terribly smart and I assume everyone must have great reasons for doing it the way they do. On the other hand, I'm not opposed to people just missing the elephant in the room and I've never heard a an actual argument for doing package naming this way. It just seems to be the de facto standard.
Logical: Naming your packages according to their business domain identity and putting every class that has to do with that vertical slice of functionality into that package.
I have never seen or heard of this, as I mentioned before, but it makes a ton of sense to me.
I tend to approach systems vertically rather than horizontally. I want to go in and develop the Order Processing system, not the data access layer. Obviously, there's a good chance that I'll touch the data access layer in the development of that system, but the point is that I don't think of it that way. What this means, of course, is that when I receive a change order or want to implement some new feature, it'd be nice to not have to go fishing around in a bunch of packages in order to find all the related classes. Instead, I just look in the X package because what I'm doing has to do with X.
From a development standpoint, I see it as a major win to have your packages document your business domain rather than your architecture. I feel like the domain is almost always the part of the system that's harder to grok where as the system's architecture, especially at this point, is almost becoming mundane in its implementation. The fact that I can come to a system with this type of naming convention and instantly from the naming of the packages know that it deals with orders, customers, enterprises, products, etc. seems pretty darn handy.
It seems like this would allow you to take much better advantage of Java's access modifiers. This allows you to much more cleanly define interfaces into subsystems rather than into layers of the system. So if you have an orders subsystem that you want to be transparently persistent, you could in theory just never let anything else know that it's persistent by not having to create public interfaces to its persistence classes in the dao layer and instead packaging the dao class in with only the classes it deals with. Obviously, if you wanted to expose this functionality, you could provide an interface for it or make it public. It just seems like you lose a lot of this by having a vertical slice of your system's features split across multiple packages.
I suppose one disadvantage that I can see is that it does make ripping out layers a little bit more difficult. Instead of just deleting or renaming a package and then dropping a new one in place with an alternate technology, you have to go in and change all of the classes in all of the packages. However, I don't see this is a big deal. It may be from a lack of experience, but I have to imagine that the amount of times you swap out technologies pales in comparison to the amount of times you go in and edit vertical feature slices within your system.
So I guess the question then would go out to you, how do you name your packages and why? Please understand that I don't necessarily think that I've stumbled onto the golden goose or something here. I'm pretty new to all this with mostly academic experience. However, I can't spot the holes in my reasoning so I'm hoping you all can so that I can move on.
For package design, I first divide by layer, then by some other functionality.
There are some additional rules:
layers are stacked from most general (bottom) to most specific (top)
each layer has a public interface (abstraction)
a layer can only depend on the public interface of another layer (encapsulation)
a layer can only depend on more general layers (dependencies from top to bottom)
a layer preferably depends on the layer directly below it
So, for a web application for example, you could have the following layers in your application tier (from top to bottom):
presentation layer: generates the UI that will be shown in the client tier
application layer: contains logic that is specific to an application, stateful
service layer: groups functionality by domain, stateless
integration layer: provides access to the backend tier (db, jms, email, ...)
For the resulting package layout, these are some additional rules:
the root of every package name is <prefix.company>.<appname>.<layer>
the interface of a layer is further split up by functionality: <root>.<logic>
the private implementation of a layer is prefixed with private: <root>.private
Here is an example layout.
The presentation layer is divided by view technology, and optionally by (groups of) applications.
com.company.appname.presentation.internal
com.company.appname.presentation.springmvc.product
com.company.appname.presentation.servlet
...
The application layer is divided into use cases.
com.company.appname.application.lookupproduct
com.company.appname.application.internal.lookupproduct
com.company.appname.application.editclient
com.company.appname.application.internal.editclient
...
The service layer is divided into business domains, influenced by the domain logic in a backend tier.
com.company.appname.service.clientservice
com.company.appname.service.internal.jmsclientservice
com.company.appname.service.internal.xmlclientservice
com.company.appname.service.productservice
...
The integration layer is divided into 'technologies' and access objects.
com.company.appname.integration.jmsgateway
com.company.appname.integration.internal.mqjmsgateway
com.company.appname.integration.productdao
com.company.appname.integration.internal.dbproductdao
com.company.appname.integration.internal.mockproductdao
...
Advantages of separating packages like this is that it is easier to manage complexity, and it increases testability and reusability. While it seems like a lot of overhead, in my experience it actually comes very natural and everyone working on this structure (or similar) picks it up in a matter of days.
Why do I think the vertical approach is not so good?
In the layered model, several different high-level modules can use the same lower-level module. For example: you can build multiple views for the same application, multiple applications can use the same service, multiple services can use the same gateway. The trick here is that when moving through the layers, the level of functionality changes. Modules in more specific layers don't map 1-1 on modules from the more general layer, because the levels of functionality they express don't map 1-1.
When you use the vertical approach for package design, i.e. you divide by functionality first, then you force all building blocks with different levels of functionality into the same 'functionality jacket'. You might design your general modules for the more specific one. But this violates the important principle that the more general layer should not know about more specific layers. The service layer for example shouldn't be modeled after concepts from the application layer.
I find myself sticking with Uncle Bob's package design principles. In short, classes which are to be reused together and changed together (for the same reason, e.g. a dependency change or a framework change) should be put in the same package. IMO, the functional breakdown would have better chance of achieving these goals than the vertical/business-specific break-down in most applications.
For example, a horizontal slice of domain objects can be reused by different kinds of front-ends or even applications and a horizontal slice of the web front-end is likely to change together when the underlying web framework needs to be changed. On the other hand, it's easy to imagine the ripple effect of these changes across many packages if classes across different functional areas are grouped in those packages.
Obviously, not all kinds of software are the same and the vertical breakdown may make sense (in terms of achieving the goals of reusability and closeability-to-change) in certain projects.
There are usually both levels of division present. From the top, there are deployment units. These are named 'logically' (in your terms, think Eclipse features). Inside deployment unit, you have functional division of packages (think Eclipse plugins).
For example, feature is com.feature, and it consists of com.feature.client, com.feature.core and com.feature.ui plugins. Inside plugins, I have very little division to other packages, although that's not unusual too.
Update: Btw, there is great talk by Juergen Hoeller about code organization at InfoQ: http://www.infoq.com/presentations/code-organization-large-projects. Juergen is one of architects of Spring, and knows a lot about this stuff.
Most java projects I've worked on slice the java packages functionally first, then logically.
Usually parts are sufficiently large that they're broken up into separate build artifacts, where you might put core functionality into one jar, apis into another, web frontend stuff into a warfile, etc.
Both functional (architectural) and logical (feature) approaches to packaging have a place. Many example applications (those found in text books etc.) follow the functional approach of placing presentation, business services, data mapping, and other architectural layers into separate packages. In example applications, each package often has only a few or just one class.
This initial approach is fine since a contrived example often serves to: 1) conceptually map out the architecture of the framework being presented, 2) is done so with a single logical purpose (e.g. add/remove/update/delete pets from a clinic). The problem is that many readers take this as a standard that has no bounds.
As a "business" application expands to include more and more features, following the functional approach becomes a burden. Although I know where to look for types based on architecture layer (e.g. web controllers under a "web" or "ui" package, etc.), developing a single logical feature begins to require jumping back and forth between many packages. This is cumbersome, at the very least, but its worse than that.
Since logically related types are not packaged together, the API is overly publicized; the interaction between logically related types is forced to be 'public' so that types can import and interact with each other (the ability to minimize to default/package visibility is lost).
If I am building a framework library, by all means my packages will follow a functional/architectural packaging approach. My API consumers might even appreciate that their import statements contain intuitive package named after the architecture.
Conversely, when building a business application I will package by feature. I have no problem placing Widget, WidgetService, and WidgetController all in the same "com.myorg.widget." package and then taking advantage of default visibility (and having fewer import statements as well as inter-package dependencies).
There are, however, cross-over cases. If my WidgetService is used by many logical domains (features), I might create a "com.myorg.common.service." package. There is also a good chance that I create classes with intention to be re-usable across features and end up with packages such as "com.myorg.common.ui.helpers." and "com.myorg.common.util.". I may even end up moving all these later "common" classes in a separate project and include them in my business application as a myorg-commons.jar dependency.
Packages are to be compiled and distributed as a unit. When considering what classes belong in a package, one of the key criteria is its dependencies. What other packages (including third-party libraries) does this class depend on. A well-organized system will cluster classes with similar dependencies in a package. This limits the impact of a change in one library, since only a few well-defined packages will depend on it.
It sounds like your logical, vertical system might tend to "smear" dependencies across most packages. That is, if every feature is packaged as a vertical slice, every package will depend on every third party library that you use. Any change to a library is likely to ripple through your whole system.
I personally prefer grouping classes logically then within that include a subpackage for each functional participation.
Goals of packaging
Packages are after all about grouping things together - the idea being related classes live close to each other. If they live in the same package they can take advantage of package private to limit visibility. The problem is lumping all your view and persitance stuff into one package can lead to a lot of classes being mixed up into a single package. The next sensible thing to do is thus create view, persistance, util sub packages and refactor classes accordingly. Underfortunately protected and package private scoping does not support the concept of the current package and sub package as this would aide in enforcing such visibility rules.
I see now value in separation via functionality becase what value is there to group all the view related stuff. Things in this naming strategy become disconnected with some classes in the view whilst others are in persistance and so on.
An example of my logical packaging structure
For purposes of illustration lets name two modules - ill use the name module as a concept that groups classes under a particular branch of a pacckage tree.
apple.model
apple.store
banana.model
banana.store
Advantages
A client using the Banana.store.BananaStore is only exposed to the functionality we wish to make available. The hibernate version is an implementation detail which they do not need to be aware nor should they see these classes as they add clutter to storage operations.
Other Logical v Functional advantages
The further up towards the root the broader the scope becomes and things belonging to one package start to exhibit more and more dependencies on things belonging to toher modules. If one were to examine for example the "banana" module most of the dependencies would be limited to within that module. In fact most helpers under "banana" would not be referenced at all outside this package scope.
Why functionality ?
What value does one achieve by lumping things based on functionality. Most classes in such a case are independent of each other with little or no need to take advantage of package private methods or classes. Refactoring them so into their own subpackages gains little but does help reduce the clutter.
Developer changes to the system
When developers are tasked to make changes that are a bit more than trivial it seems silly that potentially they have changes that include files from all areas of the package tree. With the logical structured approach their changes are more local within the same part of the package tree which just seems right.
It depends on the granularity of your logical processes?
If they're standalone, you often have a new project for them in source control, rather than a new package.
The project I'm on at the moment is erring towards logical splitting, there's a package for the jython aspect, a package for a rule engine, packages for foo, bar, binglewozzle, etc. I'm looking at having the XML specific parsers/writers for each module within that package, rather than having an XML package (which I have done previously), although there will still be a core XML package where shared logic goes. One reason for this however is that it may be extensible (plugins) and thus each plugin will need to also define its XML (or database, etc) code, so centralising this could introduce problems later on.
In the end it seems to be how it seems most sensible for the particular project. I think it's easy to package along the lines of the typical project layered diagram however. You'll end up with a mix of logical and functional packaging.
What's needed is tagged namespaces. An XML parser for some Jython functionality could be tagged both Jython and XML, rather than having to choose one or the other.
Or maybe I'm wibbling.
I try to design package structures in such a way that if I were to draw a dependency graph, it would be easy to follow and use a consistent pattern, with as few circular references as possible.
For me, this is much easier to maintain and visualize in a vertical naming system rather than horizontal. if component1.display has a reference to component2.dataaccess, that throws off more warning bells than if display.component1 has a reference to dataaccess. component2.
Of course, components shared by both go in their own package.
I totally follow and propose the logical ("by-feature") organization! A package should follow the concept of a "module" as closely as possible. The functional organization may spread a module over a project, resulting in less encapsulation, and prone to changes in implementation details.
Let's take an Eclipse plugin for example: putting all the views or actions in one package would be a mess. Instead, each component of a feature should go to the feature's package, or if there are many, into subpackages (featureA.handlers, featureA.preferences etc.)
Of course, the problem lies in the hierarchical package system (which among others Java has), which makes the handling of orthogonal concerns impossible or at least very difficult - although they occur everywhere!
I would personally go for functional naming. The short reason: it avoids code duplication or dependency nightmare.
Let me elaborate a bit. What happens when you are using an external jar file, with its own package tree? You are effectively importing the (compiled) code into your project, and with it a (functionally separated) package tree. Would it make sense to use the two naming conventions at the same time? No, unless that was hidden from you. And it is, if your project is small enough and has a single component. But if you have several logical units, you probably don't want to re-implement, let's say, the data file loading module. You want to share it between logical units, not have artificial dependencies between logically unrelated units, and not have to choose which unit you are going to put that particular shared tool into.
I guess this is why functional naming is the most used in projects that reach, or are meant to reach, a certain size, and logical naming is used in class naming conventions to keep track of the specific role, if any of each class in a package.
I will try to respond more precisely to each of your points on logical naming.
If you have to go fishing in old classes to modify functionalities when you have a change of plans, it's a sign of bad abstraction: you should build classes that provide a well defined functionality, definable in one short sentence. Only a few, top-level classes should assemble all these to reflect your business intelligence. This way, you will be able to reuse more code, have easier maintenance, clearer documentation and less dependency issues.
That mainly depends on the way you grok your project. Definitely, logical and functional view are orthogonal. So if you use one naming convention, you need to apply the other one to class names in order to keep some order, or fork from one naming convention to an other at some depth.
Access modifiers are a good way to allow other classes that understand your processing to access the innards of your class. Logical relationship does not mean an understanding of algorithmic or concurrency constraints. Functional may, although it does not. I am very weary of access modifiers other than public and private, because they often hide a lack of proper architecturing and class abstraction.
In big, commercial projects, changing technologies happens more often than you would believe. For instance, I have had to change 3 times already of XML parser, 2 times of caching technology, and 2 times of geolocalisation software. Good thing I had hid all the gritty details in a dedicated package...
It is an interesting experiment not to use packages at all (except for the root package.)
The question that arises then, is, when and why it makes sense to introduce packages. Presumably, the answer will be different from what you would have answered at the beginning of the project.
I presume that your question arises at all, because packages are like categories and it's sometimes hard to decide for one or the other. Sometimes tags would be more appreciate to communicate that a class is usable in many contexts.
From a purely practical standpoint, java's visibility constructs allow classes in the same package to access methods and properties with protected and default visibility, as well as the public ones. Using non-public methods from a completely different layer of the code would definitely be a big code smell. So I tend to put classes from the same layer into the same package.
I don't often use these protected or default methods elsewhere - except possibly in the unit tests for the class - but when I do, it is always from a class at the same layer
It depends. In my line of work, we sometimes split packages by functions (data access, analytics) or by asset class (credit, equities, interest rates). Just select the structure which is most convenient for your team.
From my experience, re-usability creates more problems than solving. With the latest & cheap processors and memory, I would prefer duplication of code rather than tightly integrating in order to reuse.