[Nexus 5 Themes and Apps] PiSpecialist:
First download the apktool from here then install the framework of android M extracted from your Rom, choose your desired mod/s and follow the instructions.

Ambient Display:

1. Decompile SystemUI.apk

2. Navigate to systemui/res/values/bools.xml and change this line:

from

<bool name="doze_display_state_supported">false</bool>
<bool name="doze_pulse_on_pick_up">false</bool>

to

<bool name="doze_display_state_supported">true</bool>
<bool name="doze_pulse_on_pick_up">true</bool>

3. Save and recompile SystemUI.apk

4. Decompile framework-res.apk

5. Navigate to framework-res/res/values/strings.xml and change this line:

from

<string name="config_dozeComponent"></string>

to

<string name="config_dozeComponent">com.android.systemui/com.android.systemui.doze.DozeService</string>

6. Save and close

7. Now in the same folder open bools.xml and change this line:

from

<bool name="config_dozeAfterScreenOff">false</bool>
<bool name="config_powerDecoupleInteractiveModeFromDisplay">false</bool>

to

<bool name="config_dozeAfterScreenOff">true</bool>
<bool name="config_powerDecoupleInteractiveModeFromDisplay">true</bool>

Save it and close

8. Now in the same folder open integers.xml and change this line:

from

<integer name="config_screenBrightnessDoze">1</integer>

to

<integer name="config_screenBrightnessDoze">17</integer>

9. Save and recompile framework-res.apk

Add Extended Power Menu:

don't ask for reboot options,soft,recovery...etc, here i just enabled the hidden power menu options in the google source code.

1. Decompile framework-res.apk

2. Navigate to framework-res/res/values/arrays.xml and change this line:

from

<string-array name="config_globalActionsList">
<item>power</item>
<item>bugreport</item>
<item>users</item>
</string-array>

to

<string-array name="config_globalActionsList">
<item>power</item>
<item>airplane</item>
<item>settings</item>
<item>lockdown</item>
<item>voiceassist</item>
<item>bugreport</item>
<item>silent</item>
<item>users</item>
</string-array>

3. Save and recompile framework-res.apk

Add center clock:

1. Decompile SystemUI.apk

2. Navigate to systemui/res/layout/status_bar.xml and add this line:

<LinearLayout android:gravity="center" android:orientation="horizontal" android:id="@id/notification_icon_area_inner" android:layout_width="fill_parent" android:layout_height="fill_parent">
<com.android.systemui.statusbar.policy.Clock android:textAppearance="@style/TextAppearance.StatusBar.Clock" android:gravity="start|center" android:id="@id/clock" android:layout_width="wrap_content" android:layout_height="fill_parent" android:singleLine="true" />
</LinearLayout>

immediatly after this line:

xmlns:systemui="http://schemas.android.com/apk/res/com.android.systemui">

and delete this line:

<com.android.systemui.statusbar.policy.Clock android:textAppearance="@style/TextAppearance.StatusBar.Clock" android:gravity="start|center" android:id="@id/clock" android:layout_width="wrap_content" android:layout_height="fill_parent" android:singleLine="true" android:paddingStart="7.0dip" />

3. Save and close

4. Navigate to systemui/res/values/dimens.xml and change this line:

from

<dimen name="keyguard_carrier_text_margin">16.0dip</dimen>

to

<dimen name="keyguard_carrier_text_margin">156.0dip</dimen>

5. Save and recompile SystemUI.apk

for every mod put your modded framework or/and system in the corresponding folder inside the attached zip(mod_hammerhead for Nexus 5 and mod_shamu for Nexus 6), flash via TWRP revovery.