docs: align project guides with current source and README conventions

[ryanbarlow97]

Project READMEs and linked guides contained stale commands, dependency requirements, test/coverage claims, and implementation details that belong in Docs. This update aligns the guides with current default-branch source and keeps source READMEs focused on features, documentation, tests and licensing.

Moves command, integration and testing manuals into project guides; corrects permission defaults, reward locking, injury healing, authentication, asset inventory descriptions and first-start behavior. Separates TLibs/VehicleFramework loader metadata from the shared Paper 1.21.10 build baseline. Private asset instructions remain in ServerAssets.

Validation:

• Audited 95 READMEs across 40 active repositories plus the workspace README; 83 README files updated.
• All 40 repository diffs pass git diff --check.
• Docs: 5 unit tests pass; 774 local links/anchors across 203 Markdown pages pass; CoreProtect MkDocs builds in strict mode.
• README audit: 597 local and active-repository link targets/anchors pass. External README URLs were checked separately.
• ServerAssets: manifest, magic and CompanionPets validators pass. TLibs: 34 Python tooling tests pass.
• Six audit agents checked source/build evidence; an independent reviewer found no actionable issues in its assigned review scope. No Minecraft/runtime validation was performed for these documentation edits.

The separate workspace Java package checker reports 18 existing namespace findings in external API test fixtures. No Java sources or checker rules are changed here.

Related source README PRs (merge this Docs update first so new guide links resolve):

• ActivityTF
• AdvancedCrafting
• Archaeo
• ArmourShop
• BarterShops
• BirdMessenger
• CompanionPets
• Cooking
• CoreProtect
• DenarEconomy
• Dowsing
• DrinkBuilder
• Games
• Gathering
• GeigerCounters
• GemInfusion
• GunsAndGadgets
• Infestations
• InteractibleFurniture
• Magic
• MarketBlock
• MusicalInstruments
• PermCleaner
• ProvinceSystem
• Recycler
• Research
• RPCharacters
• ServerAssets
• SimpleFactions
• Surgery
• TFMCCore
• TFMCWeb
• Thievery
• TLibs
• TrialRooms
• VehicleFramework
• VFBuilders
• Woodworking
• WorldBorder