Looks like this problem is fixed.

asfernandes · asfernandes · commit c218a2dbc6d1 · 2016-02-22T00:26:18.000-03:00
diff --git a/src/fbjava/src/main/java/org/firebirdsql/fbjava/Deployer.java b/src/fbjava/src/main/java/org/firebirdsql/fbjava/Deployer.java
@@ -379,7 +379,7 @@ else if (moreArgs)
 				++i;
 			}
 			else if (installPlugin)
-				doInstallPlugin();	//// FIXME: Not working with Firebird embedded in Java process.
+				doInstallPlugin();
 			else if (uninstallPlugin)
 				doUninstallPlugin();
 			else

Original file line number	Diff line number	Diff line change
`@@ -379,7 +379,7 @@ else if (moreArgs)`
`379`	`379`	`++i;`
`380`	`380`	`}`
`381`	`381`	`else if (installPlugin)`
`382`		`- doInstallPlugin(); //// FIXME: Not working with Firebird embedded in Java process.`
	`382`	`+ doInstallPlugin();`
`383`	`383`	`else if (uninstallPlugin)`
`384`	`384`	`doUninstallPlugin();`
`385`	`385`	`else`