diff --git a/phpseclib/Crypt/Base.php b/phpseclib/Crypt/Base.php
index 9566f288..43da9510 100644
--- a/phpseclib/Crypt/Base.php
+++ b/phpseclib/Crypt/Base.php
@@ -296,9 +296,9 @@ class Crypt_Base
     /**
      * Does internal cipher state need to be (re)initialized?
      *
-     * @see setKey()
-     * @see setIV()
-     * @see disableContinuousBuffer()
+     * @see Crypt_Base::setKey()
+     * @see Crypt_Base::setIV()
+     * @see Crypt_Base::disableContinuousBuffer()
      * @var bool
      * @access private
      */
@@ -1726,9 +1726,9 @@ class Crypt_Base
      *
      * - First run of encrypt() / decrypt() with no init-settings
      *
-     * @see setKey()
-     * @see setIV()
-     * @see disableContinuousBuffer()
+     * @see Crypt_Base::setKey()
+     * @see Crypt_Base::setIV()
+     * @see Crypt_Base::disableContinuousBuffer()
      * @access private
      * @internal _setup() is always called before en/decryption.
      * @internal Could, but not must, extend by the child Crypt_* class
@@ -1760,9 +1760,9 @@ class Crypt_Base
      *
      * - First run of encrypt() / decrypt()
      *
-     * @see setKey()
-     * @see setIV()
-     * @see disableContinuousBuffer()
+     * @see Crypt_Base::setKey()
+     * @see Crypt_Base::setIV()
+     * @see Crypt_Base::disableContinuousBuffer()
      * @access private
      * @internal Could, but not must, extend by the child Crypt_* class
      */
@@ -2504,7 +2504,7 @@ class Crypt_Base
     /**
      * Generates a digest from $bytes
      *
-     * @see _setupInlineCrypt()
+     * @see Crypt_Base::_setupInlineCrypt()
      * @access private
      * @param $bytes
      * @return string
diff --git a/phpseclib/Crypt/DES.php b/phpseclib/Crypt/DES.php
index 8ac1fe6b..b7332bcf 100644
--- a/phpseclib/Crypt/DES.php
+++ b/phpseclib/Crypt/DES.php
@@ -143,7 +143,7 @@ class Crypt_DES extends Crypt_Base
      * The Key
      *
      * @see Crypt_Base::key
-     * @see setKey()
+     * @see Crypt_Base::setKey()
      * @var string
      * @access private
      */
diff --git a/phpseclib/Crypt/Hash.php b/phpseclib/Crypt/Hash.php
index bc8719ec..6be2ee72 100644
--- a/phpseclib/Crypt/Hash.php
+++ b/phpseclib/Crypt/Hash.php
@@ -759,7 +759,7 @@ class Crypt_Hash
      * @access private
      * @param int $int
      * @param int $amt
-     * @see _sha256()
+     * @see Crypt_Hash::_sha256()
      * @return int
      */
     function _rightRotate($int, $amt)
@@ -775,7 +775,7 @@ class Crypt_Hash
      * @access private
      * @param int $int
      * @param int $amt
-     * @see _sha256()
+     * @see Crypt_Hash::_sha256()
      * @return int
      */
     function _rightShift($int, $amt)
@@ -789,7 +789,7 @@ class Crypt_Hash
      *
      * @access private
      * @param int $int
-     * @see _sha256()
+     * @see Crypt_Hash::_sha256()
      * @return int
      */
     function _not($int)
@@ -805,7 +805,7 @@ class Crypt_Hash
      *
      * @param int $...
      * @return int
-     * @see _sha256()
+     * @see Crypt_Hash::_sha256()
      * @access private
      */
     function _add()
diff --git a/phpseclib/Crypt/RC2.php b/phpseclib/Crypt/RC2.php
index eb41fe8f..6eb766ec 100644
--- a/phpseclib/Crypt/RC2.php
+++ b/phpseclib/Crypt/RC2.php
@@ -120,7 +120,7 @@ class Crypt_RC2 extends Crypt_Base
      * The Key
      *
      * @see Crypt_Base::key
-     * @see setKey()
+     * @see Crypt_RC2::setKey()
      * @var string
      * @access private
      */
@@ -130,9 +130,9 @@ class Crypt_RC2 extends Crypt_Base
      * The Original (unpadded) Key
      *
      * @see Crypt_Base::key
-     * @see setKey()
-     * @see encrypt()
-     * @see decrypt()
+     * @see Crypt_RC2::setKey()
+     * @see Crypt_RC2::encrypt()
+     * @see Crypt_RC2::decrypt()
      * @var string
      * @access private
      */
@@ -456,7 +456,7 @@ class Crypt_RC2 extends Crypt_Base
      *
      * Mostly a wrapper for Crypt_Base::encrypt, with some additional OpenSSL handling code
      *
-     * @see decrypt()
+     * @see Crypt_RC2::decrypt()
      * @access public
      * @param string $plaintext
      * @return string $ciphertext
@@ -479,7 +479,7 @@ class Crypt_RC2 extends Crypt_Base
      *
      * Mostly a wrapper for Crypt_Base::decrypt, with some additional OpenSSL handling code
      *
-     * @see encrypt()
+     * @see Crypt_RC2::encrypt()
      * @access public
      * @param string $ciphertext
      * @return string $plaintext
diff --git a/phpseclib/Crypt/RSA.php b/phpseclib/Crypt/RSA.php
index 58111419..8643bcc6 100644
--- a/phpseclib/Crypt/RSA.php
+++ b/phpseclib/Crypt/RSA.php
@@ -751,7 +751,7 @@ class Crypt_RSA
      * Convert a private key to the appropriate format.
      *
      * @access private
-     * @see setPrivateKeyFormat()
+     * @see Crypt_RSA::setPrivateKeyFormat()
      * @param string $RSAPrivateKey
      * @return string
      */
@@ -992,7 +992,7 @@ class Crypt_RSA
      * Convert a public key to the appropriate format
      *
      * @access private
-     * @see setPublicKeyFormat()
+     * @see Crypt_RSA::setPublicKeyFormat()
      * @param string $RSAPrivateKey
      * @return string
      */
@@ -1070,8 +1070,8 @@ class Crypt_RSA
      * Break a public or private key down into its constituant components
      *
      * @access private
-     * @see _convertPublicKey()
-     * @see _convertPrivateKey()
+     * @see Crypt_RSA::_convertPublicKey()
+     * @see Crypt_RSA::_convertPrivateKey()
      * @param string $key
      * @param int $type
      * @return array
@@ -1692,8 +1692,8 @@ class Crypt_RSA
      * Private keys can be encrypted with a password.  To unset the password, pass in the empty string or false.
      * Or rather, pass in $password such that empty($password) && !is_string($password) is true.
      *
-     * @see createKey()
-     * @see loadKey()
+     * @see Crypt_RSA::createKey()
+     * @see Crypt_RSA::loadKey()
      * @access public
      * @param string $password
      */
@@ -1717,7 +1717,7 @@ class Crypt_RSA
      *
      * Returns true on success, false on failure
      *
-     * @see getPublicKey()
+     * @see Crypt_RSA::getPublicKey()
      * @access public
      * @param string $key optional
      * @param int $type optional
@@ -1777,7 +1777,7 @@ class Crypt_RSA
      *
      * Returns true on success, false on failure
      *
-     * @see getPublicKey()
+     * @see Crypt_RSA::getPublicKey()
      * @access public
      * @param string $key optional
      * @param int $type optional
@@ -1808,7 +1808,7 @@ class Crypt_RSA
      * or if the public key was set via setPublicKey().  If the currently loaded key is supposed to be the public key this
      * function won't return it since this library, for the most part, doesn't distinguish between public and private keys.
      *
-     * @see getPublicKey()
+     * @see Crypt_RSA::getPublicKey()
      * @access public
      * @param string $key
      * @param int $type optional
@@ -1836,6 +1836,7 @@ class Crypt_RSA
      * @access public
      * @param string $algorithm The hashing algorithm to be used. Valid options are 'md5' and 'sha256'. False is returned
      * for invalid values.
+     * @return mixed
      */
     public function getPublicKeyFingerprint($algorithm = 'md5')
     {
@@ -1865,10 +1866,11 @@ class Crypt_RSA
      *
      * The private key is only returned if the currently loaded key contains the constituent prime numbers.
      *
-     * @see getPublicKey()
+     * @see Crypt_RSA::getPublicKey()
      * @access public
      * @param string $key
      * @param int $type optional
+     * @return mixed
      */
     function getPrivateKey($type = CRYPT_RSA_PUBLIC_FORMAT_PKCS1)
     {
@@ -1889,7 +1891,7 @@ class Crypt_RSA
      * Returns the private key without the prime number constituants.  Structurally identical to a public key that
      * hasn't been set as the public key
      *
-     * @see getPrivateKey()
+     * @see Crypt_RSA::getPrivateKey()
      * @access private
      * @param string $key
      * @param int $type optional
@@ -1911,6 +1913,7 @@ class Crypt_RSA
      *  __toString() magic method
      *
      * @access public
+     * @return string
      */
     function __toString()
     {
@@ -1926,6 +1929,7 @@ class Crypt_RSA
      *  __clone() magic method
      *
      * @access public
+     * @return Crypt_RSA
      */
     function __clone()
     {
@@ -2021,7 +2025,7 @@ class Crypt_RSA
     /**
      * Determines the private key format
      *
-     * @see createKey()
+     * @see Crypt_RSA::createKey()
      * @access public
      * @param int $format
      */
@@ -2033,7 +2037,7 @@ class Crypt_RSA
     /**
      * Determines the public key format
      *
-     * @see createKey()
+     * @see Crypt_RSA::createKey()
      * @access public
      * @param int $format
      */
@@ -2950,7 +2954,7 @@ class Crypt_RSA
      * If $plaintext exceeds those limits it will be broken up so that it does and the resultant ciphertext's will
      * be concatenated together.
      *
-     * @see decrypt()
+     * @see Crypt_RSA::decrypt()
      * @access public
      * @param string $plaintext
      * @return string
@@ -2996,7 +3000,7 @@ class Crypt_RSA
     /**
      * Decryption
      *
-     * @see encrypt()
+     * @see Crypt_RSA::encrypt()
      * @access public
      * @param string $plaintext
      * @return string
@@ -3038,7 +3042,7 @@ class Crypt_RSA
     /**
      * Create a signature
      *
-     * @see verify()
+     * @see Crypt_RSA::verify()
      * @access public
      * @param string $message
      * @return string
@@ -3061,7 +3065,7 @@ class Crypt_RSA
     /**
      * Verifies a signature
      *
-     * @see sign()
+     * @see Crypt_RSA::sign()
      * @access public
      * @param string $message
      * @param string $signature
diff --git a/phpseclib/Crypt/Rijndael.php b/phpseclib/Crypt/Rijndael.php
index 17bbb864..614453bf 100644
--- a/phpseclib/Crypt/Rijndael.php
+++ b/phpseclib/Crypt/Rijndael.php
@@ -156,7 +156,7 @@ class Crypt_Rijndael extends Crypt_Base
      *
      * @see Crypt_Base::cipher_name_mcrypt
      * @see Crypt_Base::engine
-     * @see isValidEngine()
+     * @see Crypt_Rijndael::isValidEngine()
      * @var string
      * @access private
      */
@@ -175,7 +175,7 @@ class Crypt_Rijndael extends Crypt_Base
     /**
      * Has the key length explicitly been set or should it be derived from the key, itself?
      *
-     * @see setKeyLength()
+     * @see Crypt_Rijndael::setKeyLength()
      * @var bool
      * @access private
      */
@@ -184,7 +184,7 @@ class Crypt_Rijndael extends Crypt_Base
     /**
      * The Key Schedule
      *
-     * @see _setup()
+     * @see Crypt_Rijndael::_setup()
      * @var array
      * @access private
      */
@@ -193,7 +193,7 @@ class Crypt_Rijndael extends Crypt_Base
     /**
      * The Inverse Key Schedule
      *
-     * @see _setup()
+     * @see Crypt_Rijndael::_setup()
      * @var array
      * @access private
      */
@@ -202,7 +202,7 @@ class Crypt_Rijndael extends Crypt_Base
     /**
      * The Block Length divided by 32
      *
-     * @see setBlockLength()
+     * @see Crypt_Rijndael::setBlockLength()
      * @var int
      * @access private
      * @internal The max value is 256 / 32 = 8, the min value is 128 / 32 = 4.  Exists in conjunction with $block_size
@@ -215,7 +215,7 @@ class Crypt_Rijndael extends Crypt_Base
     /**
      * The Key Length
      *
-     * @see setKeyLength()
+     * @see Crypt_Rijndael::setKeyLength()
      * @var int
      * @access private
      * @internal The max value is 256 / 8 = 32, the min value is 128 / 8 = 16.  Exists in conjunction with $Nk
@@ -228,7 +228,7 @@ class Crypt_Rijndael extends Crypt_Base
     /**
      * The Key Length divided by 32
      *
-     * @see setKeyLength()
+     * @see Crypt_Rijndael::setKeyLength()
      * @var int
      * @access private
      * @internal The max value is 256 / 32 = 8, the min value is 128 / 32 = 4
@@ -301,7 +301,7 @@ class Crypt_Rijndael extends Crypt_Base
      * Note: 160/224-bit keys must explicitly set by setKeyLength(), otherwise they will be round/pad up to 192/256 bits.
      *
      * @see Crypt_Base:setKey()
-     * @see setKeyLength()
+     * @see Crypt_Rijndael::setKeyLength()
      * @access public
      * @param string $key
      */
diff --git a/phpseclib/Math/BigInteger.php b/phpseclib/Math/BigInteger.php
index 4e86449b..6d626a6a 100644
--- a/phpseclib/Math/BigInteger.php
+++ b/phpseclib/Math/BigInteger.php
@@ -191,18 +191,10 @@ class Math_BigInteger
      */
     var $is_negative = false;
 
-    /**
-     * Random number generator function
-     *
-     * @see setRandomGenerator()
-     * @access private
-     */
-    var $generator = 'mt_rand';
-
     /**
      * Precision
      *
-     * @see setPrecision()
+     * @see Math_BigInteger::setPrecision()
      * @access private
      */
     var $precision = -1;
@@ -210,7 +202,7 @@ class Math_BigInteger
     /**
      * Precision Bitmask
      *
-     * @see setPrecision()
+     * @see Math_BigInteger::setPrecision()
      * @access private
      */
     var $bitmask = false;
@@ -222,8 +214,8 @@ class Math_BigInteger
      * a variable that'll be serializable regardless of whether or not extensions are being used.  Unlike $this->value,
      * however, $this->hex is only calculated when $this->__sleep() is called.
      *
-     * @see __sleep()
-     * @see __wakeup()
+     * @see Math_BigInteger::__sleep()
+     * @see Math_BigInteger::__wakeup()
      * @var string
      * @access private
      */
@@ -738,7 +730,7 @@ class Math_BigInteger
      * {@link http://php.net/language.oop5.basic#51624}
      *
      * @access public
-     * @see __clone()
+     * @see Math_BigInteger::__clone()
      * @return Math_BigInteger
      */
     function copy()
@@ -746,7 +738,6 @@ class Math_BigInteger
         $temp = new Math_BigInteger();
         $temp->value = $this->value;
         $temp->is_negative = $this->is_negative;
-        $temp->generator = $this->generator;
         $temp->precision = $this->precision;
         $temp->bitmask = $this->bitmask;
         return $temp;
@@ -775,7 +766,7 @@ class Math_BigInteger
      * call Math_BigInteger::copy(), instead.
      *
      * @access public
-     * @see copy()
+     * @see Math_BigInteger::copy()
      * @return Math_BigInteger
      */
     function __clone()
@@ -788,16 +779,13 @@ class Math_BigInteger
      *
      * Will be called, automatically, when serialize() is called on a Math_BigInteger object.
      *
-     * @see __wakeup()
+     * @see Math_BigInteger::__wakeup()
      * @access public
      */
     function __sleep()
     {
         $this->hex = $this->toHex(true);
         $vars = array('hex');
-        if ($this->generator != 'mt_rand') {
-            $vars[] = 'generator';
-        }
         if ($this->precision > 0) {
             $vars[] = 'precision';
         }
@@ -809,7 +797,7 @@ class Math_BigInteger
      *
      * Will be called, automatically, when unserialize() is called on a Math_BigInteger object.
      *
-     * @see __sleep()
+     * @see Math_BigInteger::__sleep()
      * @access public
      */
     function __wakeup()
@@ -817,7 +805,6 @@ class Math_BigInteger
         $temp = new Math_BigInteger($this->hex, -16);
         $this->value = $temp->value;
         $this->is_negative = $temp->is_negative;
-        $this->setRandomGenerator($this->generator);
         if ($this->precision > 0) {
             // recalculate $this->bitmask
             $this->setPrecision($this->precision);
@@ -1876,7 +1863,7 @@ class Math_BigInteger
      *
      * For most $modes this will return the remainder.
      *
-     * @see _slidingWindow()
+     * @see Math_BigInteger::_slidingWindow()
      * @access private
      * @param array $x
      * @param array $n
@@ -1913,7 +1900,7 @@ class Math_BigInteger
     /**
      * Modular reduction preperation
      *
-     * @see _slidingWindow()
+     * @see Math_BigInteger::_slidingWindow()
      * @access private
      * @param array $x
      * @param array $n
@@ -1931,7 +1918,7 @@ class Math_BigInteger
     /**
      * Modular multiply
      *
-     * @see _slidingWindow()
+     * @see Math_BigInteger::_slidingWindow()
      * @access private
      * @param array $x
      * @param array $y
@@ -1951,7 +1938,7 @@ class Math_BigInteger
     /**
      * Modular square
      *
-     * @see _slidingWindow()
+     * @see Math_BigInteger::_slidingWindow()
      * @access private
      * @param array $x
      * @param array $n
@@ -1972,7 +1959,7 @@ class Math_BigInteger
      * Calculates $x%$n, where $n = 2**$e, for some $e.  Since this is basically the same as doing $x & ($n-1),
      * we'll just use this function as a wrapper for doing that.
      *
-     * @see _slidingWindow()
+     * @see Math_BigInteger::_slidingWindow()
      * @access private
      * @param Math_BigInteger
      * @return Math_BigInteger
@@ -2002,7 +1989,7 @@ class Math_BigInteger
      * (x >> 1) + (x >> 1) != x / 2 + x / 2.  If x is even, they're the same, but if x is odd, they're not.  See the in-line
      * comments for details.
      *
-     * @see _slidingWindow()
+     * @see Math_BigInteger::_slidingWindow()
      * @access private
      * @param array $n
      * @param array $m
@@ -2099,7 +2086,7 @@ class Math_BigInteger
      * For numbers with more than four digits Math_BigInteger::_barrett() is faster.  The difference between that and this
      * is that this function does not fold the denominator into a smaller form.
      *
-     * @see _slidingWindow()
+     * @see Math_BigInteger::_slidingWindow()
      * @access private
      * @param array $x
      * @param array $n
@@ -2170,7 +2157,7 @@ class Math_BigInteger
      *
      * If you're going to be doing array_slice($product->value, 0, $stop), some cycles can be saved.
      *
-     * @see _regularBarrett()
+     * @see Math_BigInteger::_regularBarrett()
      * @param array $x_value
      * @param bool $x_negative
      * @param array $y_value
@@ -2251,8 +2238,8 @@ class Math_BigInteger
      * improved upon (basically, by using the comba method).  gcd($n, 2) must be equal to one for this function
      * to work correctly.
      *
-     * @see _prepMontgomery()
-     * @see _slidingWindow()
+     * @see Math_BigInteger::_prepMontgomery()
+     * @see Math_BigInteger::_slidingWindow()
      * @access private
      * @param array $x
      * @param array $n
@@ -2298,8 +2285,8 @@ class Math_BigInteger
      * Interleaves the montgomery reduction and long multiplication algorithms together as described in
      * {@link http://www.cacr.math.uwaterloo.ca/hac/about/chap14.pdf#page=13 HAC 14.36}
      *
-     * @see _prepMontgomery()
-     * @see _montgomery()
+     * @see Math_BigInteger::_prepMontgomery()
+     * @see Math_BigInteger::_montgomery()
      * @access private
      * @param array $x
      * @param array $y
@@ -2350,8 +2337,8 @@ class Math_BigInteger
     /**
      * Prepare a number for use in Montgomery Modular Reductions
      *
-     * @see _montgomery()
-     * @see _slidingWindow()
+     * @see Math_BigInteger::_montgomery()
+     * @see Math_BigInteger::_slidingWindow()
      * @access private
      * @param array $x
      * @param array $n
@@ -2389,7 +2376,7 @@ class Math_BigInteger
      *
      * Thanks to Pedro Gimeno Fortea for input!
      *
-     * @see _montgomery()
+     * @see Math_BigInteger::_montgomery()
      * @access private
      * @param array $x
      * @return int
@@ -2676,7 +2663,7 @@ class Math_BigInteger
      * @param Math_BigInteger $y
      * @return int < 0 if $this is less than $y; > 0 if $this is greater than $y, and 0 if they are equal.
      * @access public
-     * @see equals()
+     * @see Math_BigInteger::equals()
      * @internal Could return $this->subtract($x), but that's not as fast as what we do do.
      */
     function compare($y)
@@ -2699,7 +2686,7 @@ class Math_BigInteger
      * @param array $y_value
      * @param bool $y_negative
      * @return int
-     * @see compare()
+     * @see Math_BigInteger::compare()
      * @access private
      */
     function _compare($x_value, $x_negative, $y_value, $y_negative)
@@ -2735,7 +2722,7 @@ class Math_BigInteger
      * @param Math_BigInteger $x
      * @return bool
      * @access public
-     * @see compare()
+     * @see Math_BigInteger::compare()
      */
     function equals($x)
     {
@@ -3297,7 +3284,7 @@ class Math_BigInteger
      *
      * If the current number is odd it'll be unchanged.  If it's even, one will be added to it.
      *
-     * @see randomPrime()
+     * @see Math_BigInteger::randomPrime()
      * @access private
      */
     function _make_odd()
@@ -3547,7 +3534,7 @@ class Math_BigInteger
      *
      * @param Math_BigInteger
      * @return Math_BigInteger
-     * @see _trim()
+     * @see Math_BigInteger::_trim()
      * @access private
      */
     function _normalize($result)
@@ -3727,7 +3714,7 @@ class Math_BigInteger
      *
      * The ability to DER-encode integers is needed to create RSA public keys for use with OpenSSL
      *
-     * @see modPow()
+     * @see Math_BigInteger::modPow()
      * @access private
      * @param int $length
      * @return string
diff --git a/phpseclib/Net/SSH1.php b/phpseclib/Net/SSH1.php
index 21c305a6..a1fb2b4f 100644
--- a/phpseclib/Net/SSH1.php
+++ b/phpseclib/Net/SSH1.php
@@ -437,7 +437,7 @@ class Net_SSH1
     /**
      * Log Boundary
      *
-     * @see Net_SSH1::_format_log
+     * @see Net_SSH1::_format_log()
      * @access private
      */
     var $log_boundary = ':';
@@ -445,7 +445,7 @@ class Net_SSH1
     /**
      * Log Long Width
      *
-     * @see Net_SSH1::_format_log
+     * @see Net_SSH1::_format_log()
      * @access private
      */
     var $log_long_width = 65;
@@ -453,7 +453,7 @@ class Net_SSH1
     /**
      * Log Short Width
      *
-     * @see Net_SSH1::_format_log
+     * @see Net_SSH1::_format_log()
      * @access private
      */
     var $log_short_width = 16;
diff --git a/phpseclib/Net/SSH2.php b/phpseclib/Net/SSH2.php
index 07d7d452..4a89458f 100644
--- a/phpseclib/Net/SSH2.php
+++ b/phpseclib/Net/SSH2.php
@@ -1942,7 +1942,7 @@ class Net_SSH2
      * @param mixed $password
      * @param mixed $...
      * @return bool
-     * @see _login
+     * @see Net_SSH2::_login()
      * @access public
      */
     function login($username)
@@ -1958,7 +1958,7 @@ class Net_SSH2
      * @param mixed $password
      * @param mixed $...
      * @return bool
-     * @see _login_helper
+     * @see Net_SSH2::_login_helper()
      * @access private
      */
     function _login($username)