docs: Fix incorrect paths, obsolete flags, and missing BIP39 recovery info

[Copilot]

Documentation audit revealed broken references, non-existent flag documentation, and outdated recovery instructions.

Path Corrections

• docs/04-reference/ → docs/04-troubleshooting/
• docs/05-development/{doctor-command,ci-cd,branch-workflow} → docs/05-operations/health-checks, docs/06-development/{ci-cd,branch-workflow}
• specs/003-bip39-mnemonic-based/ → specs/archive/003-bip39-mnemonic-based/

Removed Non-Existent Flags

• --no-keychain (never implemented; keychain disabled via OS credential manager)
• --no-audit (never implemented; audit disabled by default, enabled with --enable-audit)

BIP39 Recovery Documentation

Updated FAQ sections to reflect recovery capability:

# Forgot password? Use recovery phrase (if vault initialized with it)
pass-cli change-password --recover

# Recovery phrases generated by default since recent versions
pass-cli init --no-recovery  # Skip if desired (not recommended)

Minor Fixes

• Standardized config file extension to .yml (code creates config.yml, one doc referenced config.yaml)

Original prompt

please review all the documentation and make sure that we aren't missing anything, or making reference to things that don't exist (or might be obsolete)

The user has attached the following file paths as relevant context:

• docs

Created from VS Code via the GitHub Pull Request extension.

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[arimxyer]

Closing to create a cleaner PR without duplicate content