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I've just used Michael's notes (see comments section below) - here are some updated notes based on my experience.
Misc. Details of my reference project (called "corporate")
(called "corporate")
1. MSSQL database
2. Active Directory for authentication
a. My site contains modifications to security logic. (packages/security).
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12. Launch Farcry updater at http://intranet4.XXXX.com.au/farcry/updates/
a. Use local farcry login rather than AD (check dmUsers table, mine was u:farcry/p:farcry)
i. (This may also work, I haven't tried it: "If you can not reach the updater comment out lines 39 \-51 in /Admin/Application.cfm "which checks to see if the person has general admin permissions". Be sure uncomment this when done\!")
13. Apply update for b400, click Deploy
14. Return to /farcry/updates
15. Apply update for b401, click Deploy
a. You may be able to deploy both at once, I haven't tried it.
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Apply your modifications / Deploy Types (this section i'm not sure about - in progress)
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1. Copy everything from [OldProject]\customadmin\ to [NewProject]\customadmin
2. Copy everything from [OldProject]\packages\ to [NewProject]\packages
a. Rules
b. Types
c. System
d. Change all instances of "/farcry/farcry_core/" to "/farcry/core/"
e. Change all instances of "/farcry/fourq/" to "/farcry/core/packages/fourq/"
f. Change all instances of "farcry.farcry_core" to "farcry.core"
3. Log in to Admin (http://intranet4.XXXX.com.au/farcry)
4. Go to Admin > COAPI > Type Classes and deploy / repair as necessary.
a. Turning off CF debugging will make this quicker.
5. Go to Admin > COAPI > Rule Classes and deploy / repair as necessary.
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