Renamed all .inc PHP files to .php and replaced all .inc calls

Because .inc style is deprecated and also dangerious as often not setup
correctly on the server all .inc files have been renamed to .php files.

All internall calls have been udpated.

.phan/config.php

@@ -0,0 +1,81 @@
+<?php
+
+use Phan\Config;
+
+/**
+ * This configuration will be read and overlaid on top of the
+ * default configuration. Command line arguments will be applied
+ * after this file is read.
+ *
+ * @see src/Phan/Config.php
+ * See Config for all configurable options.
+ *
+ * A Note About Paths
+ * ==================
+ *
+ * Files referenced from this file should be defined as
+ *
+ * ```
+ *   Config::projectPath('relative_path/to/file')
+ * ```
+ *
+ * where the relative path is relative to the root of the
+ * project which is defined as either the working directory
+ * of the phan executable or a path passed in via the CLI
+ * '-d' flag.
+ */
+return [
+    // If true, missing properties will be created when
+    // they are first seen. If false, we'll report an
+    // error message.
+    "allow_missing_properties" => true,
+
+    // Allow null to be cast as any type and for any
+    // type to be cast to null.
+    "null_casts_as_any_type" => true,
+
+    // Backwards Compatibility Checking
+    'backward_compatibility_checks' => false,
+
+    // Run a quick version of checks that takes less
+    // time
+    "quick_mode" => false,
+
+    // Only emit critical issues to start with
+    // (0 is low severity, 5 is normal severity, 10 is critical)
+    "minimum_severity" => 10,
+
+    // A list of directories that should be parsed for class and
+    // method information. After excluding the directories
+    // defined in exclude_analysis_directory_list, the remaining
+    // files will be statically analyzed for errors.
+    //
+    // Thus, both first-party and third-party code being used by
+    // your application should be included in this list.
+    'directory_list' => [
+         // Change this to include the folders you wish to analyze
+         // (and the folders of their dependencies)
+         'www',
+         // To speed up analysis, we recommend going back later and
+         // limiting this to only the vendor/ subdirectories your
+         // project depends on.
+         // `phan --init` will generate a list of folders for you
+         //'www/vendor',
+    ],
+
+    // A list of directories holding code that we want
+    // to parse, but not analyze
+    "exclude_analysis_directory_list" => [
+         'www/vendor',
+		 'www/lib/FileUpload',
+		 'www/lib/pChart',
+		 'www/lib/pChart2.1.4',
+		 'www/lib/Smarty',
+		 'www/lib/smarty-3.1.30',
+		 'www/templates_c',
+		 'www/log',
+		 'www/tmp',
+		 'www/cache',
+		 'www/media',
+    ],
+];