The protected file system is first initialized by function pal_linux_main (in db_main.c).

PF initialization

The init function is init_protected_files in enclave_pf.c.

int init_protected_files(void) {
    int ret;
    pf_debug_f debug_callback = NULL;

#ifdef DEBUG
    debug_callback = cb_debug;
#endif

    pf_set_callbacks(cb_read, cb_write, cb_truncate, cb_aes_gcm_encrypt, cb_aes_gcm_decrypt,
                     cb_random, debug_callback);

    /* if wrap key is not hard-coded in the manifest, assume that it was received from parent or
     * it will be provisioned after local/remote attestation; otherwise read it from manifest */
    char* protected_files_key_str = NULL;
    ret = toml_string_in(g_pal_state.manifest_root, "sgx.protected_files_key",
                         &protected_files_key_str);
    if (ret < 0) {
        log_error("Cannot parse \'sgx.protected_files_key\' "
                  "(the value must be put in double quotes!)\n");
        return -PAL_ERROR_INVAL;
    }

    if (protected_files_key_str) {
        if (strlen(protected_files_key_str) != PF_KEY_SIZE * 2) {
            log_error("Malformed \'sgx.protected_files_key\' value in the manifest\n");
            free(protected_files_key_str);
            return -PAL_ERROR_INVAL;
        }

        memset(g_pf_wrap_key, 0, sizeof(g_pf_wrap_key));
        for (size_t i = 0; i < strlen(protected_files_key_str); i++) {
            int8_t val = hex2dec(protected_files_key_str[i]);
            if (val < 0) {
                log_error("Malformed \'sgx.protected_files_key\' value in the manifest\n");
                free(protected_files_key_str);
                return -PAL_ERROR_INVAL;
            }
            g_pf_wrap_key[i / 2] = g_pf_wrap_key[i / 2] * 16 + (uint8_t)val;
        }

        free(protected_files_key_str);
        g_pf_wrap_key_set = true;
    }

    if (register_protected_files() < 0) {
        log_error("Malformed protected files found in manifest\n");
    }

    return 0;
}

Modify this function if RA/LA to pass the key to PFs

1. Set callback functions which will be invoked for encryption and decryption (when are they called?)
2. Read PF key from manifest
3. Register protected files

Open in Graphene SGX

It will check if the file to open is a PF first. See code in db_files.c:

static int file_open(PAL_HANDLE* handle, const char* type, const char* uri, int access, int share,
                     int create, int options) {
// MISSING CODE ...

        pf = load_protected_file(path, (int*)&hdl->file.fd, st.st_size, pf_mode, pf_create, pf);
        if (pf) {
            pf->refcount++;
            if (pf_mode & PF_FILE_MODE_WRITE) {
                pf->writable_fd = fd;
            }
        } else {

// MISSING CODE ...

See also Graphene-SGX PF Implementation for more details.