Here is a first attempt at implementing the Pairtree filesystem hierarchy for Fedora:

package fedora.server.storage.lowlevel;

import java.io.File;
import java.util.Map;

import fedora.server.errors.LowlevelStorageException;

/**
 * @author Chris Beer
 */
class PairtreePathAlgorithm
        extends PathAlgorithm {

    private final String storeBase;

    private static final String SEP = File.separator;

    public PairtreePathAlgorithm(Map configuration) {
        super(configuration);
        storeBase = (String) configuration.get("storeBase");
    }

    @Override
    public final String get(String pid) throws LowlevelStorageException {
        return format(pid);
    }

    public String format(String pid) throws LowlevelStorageException {
        String pt = to_pairtree(pid);
		return storeBase + pt + "obj" + SEP + pid;
    }

    private String to_pairtree(String s) {
		String pt = SEP;
		String src = escape(s);

		int i = 0;
		while(i < src.length()) {
			pt += src.substring(i, i+2) + SEP;
            i+= 2;
		}

		if(i < src.length()) {
			pt += src.substring(i);
		}

		return pt;
    }
    private String escape(String s) {
		/*
		 Fedora PIDs do not support non-visible ASCII or the characters below,
		 so we skip hex encoding:
		 "   hex 22           <   hex 3c           ?   hex 3f
		 *   hex 2a           =   hex 3d           ^   hex 5e
		 +   hex 2b           >   hex 3e           |   hex 7c
		 ,   hex 2c
		 */
		return s.replace("/", "+").replace(":", "+").replace(".", ",");
    }
}

See also: http://gist.github.com/280020

This basic services replaces the Timestamp Path algorithm for FOXML storage and creates a minimally compliant Pairtree. A better implementation could add:

• Splitting Fedora datastreams into individual files on the filesystem. A first step would be to implement an appropriate managed content mapper
• Add the appropriate identifier cleaning specified in §3. Much of this was omitted in this implementation, with the assumption that the repository core would handle identifier validation
• The implementation should support pairtree initialization (§4). The current assumption is the repository maintainer would pre-establish a pairtree hierarchy for Fedora to populate. To do this properly, I think one would need to override the DefaultLowlevelStorageModule to add an initialization step.