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The uigen.exe config file is the configuration file for uigen.exe.
It specifies "placeholders" and their values, which uigen.exe uses in
the templates. You can find the sample uigen.exe config file
here: sample uigen.exe configuration file. As always, it assumes
canonical project structure, and that the re-motion framework is
located in a sub-directory of the solution, as explained here:
PhoneBook project structure.

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The template attribute contains the path to the uigen.exe master file,
always TabbedEditor.xml.

• templateRoot: which set of templates to use
  for generating the web application project.

For re-motion version 1.13.6. and lower, these directories
are located under the Remotion directory, the root directory
of the re-motion distribution. Since uigen.exe can only
handle absolute paths, you must adapt them to your particular
location of that directory.

• targetRoot: This is the solution root, not the root directory
  for the web project, i.e. the top-level directory for all your
  Visual Studio sub-projects.

Just as the name suggests, the namespace settings are namespaces, NOT
paths:

• projectNameSpaceRoot: namespace of the web application project
• domainNameSpaceRoot: namespace of the domain project

Visual Studio mildly enforces that the directory name of a project
is the same as the namespace, so this might not matter if you follow
this convention. However, if you don't, make sure that you specified
the namespace.

Instead of a listing with complicated syntactic variables, here
is an illustration of what is which, with the PhoneBook project
as example:

Placeholders

<replace from="$key$" to="value" />

<replace from="$RemotionAssembly$" to="\PhoneBook\Remotion\net-3.5\bin\Debug" />
<!-- RemotionAssembly and WxeEngine are always the same, so... !-->
<replace from="$WebClientAssembly$" to="$RemotionAssembly$" />

• $ReferencesDir$: the name of the directory in
  the web application project for storing the
  references to the domain- and re-motion assemblies
  . By convention, this node is named "References" in
  Visual Studio, so that's probably what you will use
  for the placeholder value.
• $DomainProjectName$: the name of the directory with the
  domain project in Visual Studio (not to be confused with the
  namespace)
• $DomainProjectAssembly$: The name of the domain assembly
  that shall be inspected by uigen.exe (i.e. where to find
  the domain object classes, without ".dll")
• $WebProjectName$: the name of the directory with the web application
  project in Visual Studio. (generated by uigen.exe.)
• $WebClientAssembly$: the name of the assembly that is the
  target of the web project's target. (i.e. the .dll-product showing up
  in bin\Debug or bin\Release after a compile and link).
• $RemotionAssembly$: a better name would be $RemotionAssemblyDirectories $RemotionAssemblyDirectories$.
  It is the path to the bin\Debug or bin\Release directory
  where the re-motion framework's binary assemblies can be found.
• $WxeEngine$: where the re-call code generator WxeGen.exe can
  be found. This has been introduced for developers who might want to
  use an alternative WxeGen.exe. Since WxeGen.exe is part of
  the re-motion framework, its location is always the same as that
  of the other re-motion assemblies (see previous item, $RemotionAssembly$.
• $STRONG_SUPPLEMENT$: a VERY important placeholder for specifying the
  framework's version. re-motion, and by extension, uigen.exe insist
  on complete strong names.
  • NOT ENOUGH: Remotion.dll
  • USE STRONG NAME: Remotion.dll, Version=1.13.6.2, Culture=neutral, PublicKeyToken=fee00910d6e5f53b
• $DomainProjectGuid$: The project GUID you find in the domain project's
  .csproj file. This GUID is included in the web project's (web client's)
  .csproj file, but not checked by anyone. Use a syntactically valid Guid,
  nobody will bother you.
• $USER_APPNAME$: a string with the display name of the
  generated web application
• $USER_DEFAULT_ASPX_TOPIC$: a string to be shown on the default.aspx
  page showing the Start link to aid the user (the string
  usually says "To start the application, just click 'Start'")
  This is harder to explain than to demonstrate. Click here and
  you will easily understand it: FIXME
• $USER_DEFAULT_STARTPAGES$: an invocation of the re-call
  function to be called when the user clicks "Start" (or equivalent).
  (try Try it out with the online PhoneBook)
• $USER_STORAGEPROVIDER$: the name of the storage-provider, as
  declared in the web project's Web.config file (generated by
  uigen.exe)
• $USER_CATALOGNAME$: the name of the database (and the
  identifier for the connection string) in the web project's
  Web.config file (generated by uigen.exe) – this should be
  the same as specified for dbschema.exe's App.Config,
  explained here: using dbschema.exe
• $USER_STATUSBAR$: legacy placeholder, always set to "yes"
• $USER_CLASSIC_APPSTYLE$: legacy placeholder, always set to "no"

See also

This tech-note explains what uigen.exe does:

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What uigen.exe does