Right, I think I'm getting somewhere!

The offending code is in the Examine package Projects\Examine\LuceneEngine\Config\IndexSet.cs:

public DirectoryInfo IndexDirectory
{
    get
    {
        //TODO: Get this out of the index set. We need to use the Indexer's DataService to lookup the folder so it can be unit tested. Probably need DataServices on the searcher then too

        //we need to de-couple the context
        if (HttpContext.Current != null)
            return new DirectoryInfo(HttpContext.Current.Server.MapPath(this.IndexPath));
        else if (HostingEnvironment.ApplicationID != null)
            return new DirectoryInfo(HostingEnvironment.MapPath(this.IndexPath));
        else
            return new DirectoryInfo(this.IndexPath);
    }
}

...which basically means that you can either provide a ~/ app rooted path, OR a physical path, but that's it - you can't provide a custom resolver - which would be GREAT, if any Examine core devs read this ;)

I don't really like providing physical paths, but in order to limit this to your reindexing service, and therefore hopefully keeping the site itself working if moved, you can create a duplicate of your ExamineIndex.config, replace all paths in there with physical ones, and then using that instead in the config file for the console app.

Note that you do need the Umbraco indexes in the new file as well as your custom one as the manager always creates the default indexes. Or one, anyway, now it's working I've kind of lost the desire to look any more.

The way it works is the console app sits in the application root along with a configuration file that loads all required dependencies including the new physically rooted ExamineIndex.config; this can then be called via a System.Diagnostics.Process to start asynchronous processing from a web page - in which case it runs as the AppPool Identity - or you can run it from the Task Scheduler with an identity of your choosing.

Here is the console application config file; you can see it configuring required settings for my application and task queue, connection strings, everything needed to get Examine working, everything to make it look in the website /bin folder for support assemblies, and because I am indexing members, the system.web section to allow the membership framework to function when I load members to index. You can safely ignore this whole section unless you need to set up custom membership provides yourself.

Long post, but I'm hoping this will prove useful to someone!

<?xml version="1.0" encoding="utf-8"?>
<configuration>

    <configSections>
        <section name="MyApplicationSettings" type="MyApplication.Settings, MyApplication" />
        <section name="ActionQueueSettings" type="cFront.Scheduling.ActionQueueSettings, cfActionQueue" />
        <section name="Examine" type="Examine.Config.ExamineSettings, Examine" requirePermission="false" />
        <section name="ExamineLuceneIndexSets" type="UmbracoExamine.Config.ExamineLuceneIndexes, UmbracoExamine" requirePermission="false" />
    </configSections>

    <MyApplicationSettings configSource="config\MyApplicationSettings.config" />    
    <ActionQueueSettings configSource="config\ActionQueueSettings.config" />

    <Examine configSource="config\ExamineSettings.config" />
    <ExamineLuceneIndexSets configSource="config\ExamineIndex_QUEUE_PROCESS.config" />

    <appSettings configSource="config\appSettings.config" />

    <connectionStrings>
        <add name="AppMainConnection" connectionString="YOUR CONNECTION STRING" />
    </connectionStrings>

    <runtime>
        <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
            <probing privatePath="bin"/>
        </assemblyBinding>
    </runtime>

    <system.web>
        <!-- Membership Provider - Simplified user table with bcrypt hashing -->
        <membership defaultProvider="BCryptMembershipProvider" userIsOnlineTimeWindow="15">
            <providers>
                <clear />
                <add name="BCryptMembershipProvider" type="cFront.Web.Security.BCryptMembershipProvider, cfBCryptMembershipProvider" useBuiltInLogging="1" connectionStringName="AppMainConnection" />
            </providers>
        </membership>
        <!-- Roles Provider - Simplified user table with bcrypt hashing -->
        <roleManager enabled="true" defaultProvider="BCryptRoleProvider">
            <providers>
                <clear />
                <add name="BCryptRoleProvider" type="cFront.Web.Security.BCryptRoleProvider, cfBCryptMembershipProvider" connectionStringName="AppMainConnection" availableRoles="SuperUser,Administrator,User" />
            </providers>
        </roleManager>

    </system.web>
</configuration>