The class filters file (passed as first argument) with system environment entries (properties) to standard out. If file name ends with .xml or .properties it applies proper escaping.

FileEnvFilter.java

import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.PrintStream;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

/**
 * The class filters file (passed as first argument) with system environment entries to standard out.
 * If file name ends with .xml or .properties it applies proper escaping.
 * @author Witold Szczerba
 */
public class FileEnvFilter {

    private static final Pattern ENV_PATTERN = Pattern.compile("\\$\\{?([a-zA-Z_]+)\\}?");

    public static void main(String[] args) throws Exception {
        if (args.length != 1) {
            error("Invalid parameters count: " + args.length + ".\n"
                    + "One parameter (source file) is required.");
        }
        String sourceName = args[0];
        try (BufferedReader src = new BufferedReader(new FileReader(sourceName))) {
            new FileEnvFilter(System.getenv(), sourceName, src, System.out).filter();
        } catch (FileNotFoundException ex) {
            error("Cannot find file: " + sourceName);
        }
    }

    private static void error(String message) {
        System.err.append(message);
        System.exit(1);
    }

    private final Map<String, String> environment;

    private final String sourceName;

    private final BufferedReader source;

    private final PrintStream out;

    public FileEnvFilter(Map<String, String> environment, String sourceName, BufferedReader source, PrintStream out) {
        this.environment = environment;
        this.source = source;
        this.out = out;
        this.sourceName = sourceName;
    }

    public void filter() throws Exception {
        String line;
        while ((line = source.readLine()) != null) {
            int previousEnd = 0;
            Matcher matcher = ENV_PATTERN.matcher(line);
            while (matcher.find()) {
                String key = matcher.group(1);
                String value = valueOf(key);
                out.append(line, previousEnd, matcher.start());
                out.append(value);
                previousEnd = matcher.end();
            }
            if (previousEnd < line.length()) {
                out.append(line, previousEnd, line.length());
            }
            out.append('\n');
        }
    }

    private String valueOf(String key) {
        String value = environment.get(key);
        return value == null ? "" : escapeValue(value);
    }

    private String escapeValue(String value) {
        if (sourceName.endsWith(".xml")) {
            return escapeXML(value);
        }
        if (sourceName.endsWith(".properties")) {
            return escapeProperties(value);
        }
        return value;
    }

    private String escapeXML(String value) {
        return value //watch out, the '&' must be first!
                .replace("&", "&amp;")
                .replace("\"", "&quot;")
                .replace("<", "&lt;")
                .replace(">", "&gt;");
    }

    private String escapeProperties(String value) {
        return value;
    }
}