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Spoiler Warning
HQ Complex - calculations and supply techniques

-How much resource?
-Limit the wares on HQ
-Transport the wares to HQ
-Sample Complex

Introduction: This site explains how to plan a complex to supply your HQ non-stop. The numbers on this site is based on the patch 2.0.02, which requires only the half amount of microchips than in 2.0.01.

First of all, you have a HQ from the Bala Gi Missions. In this HQ, you can reverse engineer any ship in the universe, get the blueprint and build own ships - but to build (and repair), you will need resources in form of credits and various wares. If you only build few small ships, you will probably never need an own complex for the HQ and can ignore this site. But once if you build and repair capital class ships or the M7, you will run shortly out of resource because the NPC stations can't constantly offer resources. This would also increase the cost of the production.

How much resource? Well, as first take a look on the modified HQ Construction Chart (converted in OpenDocument, the original Excel file by Dave Toome can be found here: Exogenesis.co.uk, forum thread). On the first look, it looks like you need a huge amount of wares to produce M2, TL or M7, you could never collect. Well that's right, if you want to collect all wares at one time. But the production time is increasing for all ships in proportion to the required resources. That means the number of wares you need for a certain time period isn't that high at all - it's enough if you can refill the used resources in the production time of a ship, which can be hours and even days.

In detail (in reference to the construction chart file, line 204):
    Max. resource to build any ship:
    ECell ................ 100.800
    Ore ..................   4.200
    Teladianium ..........   3.150
    Silicon Wafers .......   3.150
    Raster Oil ...........   2.100
    Microchips ...........   1.050
    Cloth Rimes ..........   1.050
    Quantum Tubes ........   1.050
    Computer Components ..   1.050
    Crystals .............   1.050
    (Nividium ............     116)

    Max. resource per minute:
    ECell ................ 28,2
    Ore ..................  1,2
    Teladianium ..........  0,9
    Silicon Wafers .......  0,9
    Raster Oil ...........  0,6
    Microchips ...........  0,3
    Cloth Rimes ..........  0,3
    Quantum Tubes ........  0,3
    Computer Components ..  0,3
    Crystals .............  1,7
    (Nividium ............  0,1)
So you don't need to produce for example 2100 Microchips at once (= 53 Chip Plants). It's enough to produce only 0,3 per minute (= 2 Chip Plants). Now take a look on the Complex Calculator and calculate how many stations you need to produce the required wares for the HQ. That would result in:
    Required stations:
    Silicon Mines*
    Crystal Fab*
    Solar Power Plant*
    Ore Mine (>1,2 Ore/Min)
    Primary+Seconday Food Fab for Crystal,Chip,QTube,Computer
    1x Rimes Factory M + Wheat Farm M
    1x Raster Refinery M + Chelt Space Aquarium M
    1x Teladianium Foundry M
    2x Chip Plant
    1x Quantum Tube Fab
    1x Computer Plant

    * for closed cycle and overproduction for HQ
Now it's up to you to build a self-supplying complex capable of producing all these wares. If you don't know how to plan such a complex, please use the Complex Calculator or any other complex planning tool.

Limit the wares on HQ: Before transporting wares to the HQ, we need to limit the number of each wares on the HQ. Otherwise an automated transport will store uncontrolled until the HQ cargo is full - and we don't want 500k ECell on the HQ. So we use the Dockware Manager: This number is enough to build & repair any ship (actually twice of the "max. wares" list above):
    Dockware Manager, Ware Limit:
    ECell ................ 201.600
    Ore ..................   8.400
    Teladianium ..........   6.300
    Silicon Wafers .......   6.300 
    Raster Oil ...........   4.200
    Microchips ...........   2.100
    Cloth Rimes ..........   2.100
    Quantum Tubes ........   2.100
    Computer Components ..   2.100
    Crystals .............   2.100
HQ -> Station Commands -> Set ware storage space:

Important: Not all scripts are checking the DockWare limits. CLS MK1 does, but CLS MK2/UT/AI ships don't. Therefore you need lower the price of all products on the HQ something between (average - 1) and the minimum to prevent the HQ flooded with wares. It's also recommended to disallow trading with AI at all.

Transport the wares to HQ: Now all wares are available for the HQ and they have to be transported regularly to the HQ. Why regularly? The 2 Chip Plants from above example can only hold 80 Microchips on their station, so you need to transport them regularly to the HQ with it's 500k cargo.

The most simple way is to use a TS with Commodity Logistics Software (CLS) MK1. You will need a trained pilot to be able to supply the HQ with all wares in one ship. If you don't have such pilot, I recommend you this
tutorial to train CLS pilots. Once you have a Freight Pilot, use this setup:

-Select the complex as homebase of the TS
-TS -> special commands -> CLS add/remove ware -> <ware>, 0 (repeat for all 10 wares)
-TS -> special commands -> CLS add/remove station -> HQ
-TS -> Trade -> Start internal Commodity Logistics

To check the setup: CLS add/remove station -> homebase and read the incoming message. It should look like this:

That's it!
The TS will auto-transfer all wares to the HQ up to the ware limit. In the case you don't produce/repair on the HQ, the complex can keep running: set the station trading range to 50 sectors, add an another TS with Freight Pilot to the complex and enable the Commercial Agent (CAG) in the trading menu - all the overproduction will be sold and helps you getting credits to produce new ships on the HQ.

Sample Complex: Here's a example from one of my games. Note it has overproduction in all wares for more stability in the production cycle and for selling with CAG. If you only supply the HQ, you'll need less stations.
    closed cycle:
    - Silicon Mines producing 25 wafers per min
    - Ore Mine producing 1,5 ore per min
    - 14x Crystal Fab M (Argon)
    - 8x Cahoona Bakery L (Argon)
    - 9x Cattle Ranch L (Argon)
    - 2x XL and 1x L Solar Power Plant (Argon)

    attached on closed cycle:
    - 1x Rimes Factory L (Argon)
    - 3x Wheat Farm M (Argon)
    - 1x Raster Refinery L (Split)
    - 3x Chelt Space Aquarium M (Split)
    - 1x Teladianium Foundry L (Teladi)
    - 3x Chip Plant (Argon)
    - 1x Quantum Tube Fab (Argon)
    - 1x Computer Plant (Argon)