TL;DR It's up to the developer to pick which pieces of the app are signed and whether or not tampering with those pieces results in any actions when the app is launched. You have to use trial and error to figure it out on an app-by-app basis.
It is largely up to the developer to decide which components in their application bundle are represented in the seal that gets signed before they deliver their application. Anything in the seal is effectively tamper-proof as it's mostly impossible to modify these things without changing their hash signatures. But that's doesn't actually mean you can't tamper with them.
The Apple Developer guide has this to say about what you should sign:
You should sign every executable in your product, including
applications, tools, hidden helper tools, utilities and so forth.
Signing an application bundle covers its resources, but not its
subcomponents such as tools and sub-bundles. Each of these must be
signed independently.
If your application consists of a big UI part with one or more little
helper tools that try to present a single face to the user, you can
make them indistinguishable to code signing by giving them all the
exact same code signing identifier. (You can do that by making sure
that they all have the same CFBundleIdentifier value in their
Info.plist, or by using the -i option in the codesign command, to
assign the same identifier.) In that case, all your program components
have access to the same keychain items and validate as the same
program. Do this only if the programs involved are truly meant to form
a single entity, with no distinctions made.
A universal binary (bundle or tool) automatically has individual
signatures applied to each architecture component. These are
independent, and usually only the native architecture on the end
user's system is verified.
In the case of installer packages (.pkg and .mpkg bundles), everything
is implicitly signed: The CPIO archive containing the payload, the
CPIO archive containing install scripts, and the bill of materials
(BOM) each have a hash recorded in the XAR header, and that header in
turn is signed. Therefore, if you modify an install script (for
example) after the package has been signed, the signature will be
invalid.
You may also want to sign your plug-ins and libraries. Although this
is not currently required, it will be in the future, and there is no
disadvantage to having signatures on these components.
Depending on the situation, codesign may add to your Mach-O executable
file, add extended attributes to it, or create new files in your
bundle's Contents directory. None of your other files is modified.
Also from here it's not necessarily true that having an invalid signature for an application means it will fail to launch. The page says:
It is up to the system or program that is launching or loading signed
code to decide whether to verify the signature and, if it does, to
determine how to evaluate the results of that verification.
An application may choose to allow modifications.
Your best bet is a trial-and-error approach with any application you're trying to modify. It may work, it may not. There's no always-true answer that can be given.
If an app has been signed you can look for a Contents/CodeResources file or a Contents/_CodeSignature/CodeResources file in the bundle. This file lists all the signed components and their expected hash values in the bundle. It's a good place to start understanding what pieces of the application a developer deems critical enough to watch for changes.
Data containing a file's original location before being placed in the Trash is keep in the .DS_Store file in the ~/.Trash folder.
Since the trash folder is hidden it can not normally be found using the finder application. The easiest way to find this file is by using the Terminal and entering the following commands.
$cd ~/.Trash
$open -e .DS_Store
This will open the file in TextEdit. From there you should be able to quickly search for the file by its name and its original path.
Its seems that files in .DS_Store follow the pattern of:
FILE_NAME ptbLustr ORIGINAL_PATH_TO_FILE
Note spaces are added just for readability.
Best Answer
You can check a file by issuing the following command in Terminal:
There is a free tool that implements the functions of the codesign command and extends it with a nice GUI. It's called RB App Checker (on the App Store) as well as a site describing the program http://brockerhoff.net/RB/AppCheckerLite/
I've not needed anything but these two tools for checking code signing on OS X so hopefully they fit your needs. Do check out the AppChecker if your Mac doesn't have codesign (some older ones needed Xcode to get that tool before gatekeeper shipped).
As to how you would know, the OS will show untrusted apps as dim and with a generic icon until the gatekeeper process approves a bundle to run - but that code could still be signed so you can't rely on a visual clue to necessarily tell if some code has or has not been signed - especially considering that gatekeeper could be disabled on a given Mac.