fix(brain): align Windows getCleoHome with env-paths Data subdir

[calabresejordan-Caljord]

Target branch

• develop -- Normal feature/fix (default)
• main -- Hotfix only (bypasses develop, requires back-merge to develop after)

Note on target: I'd normally target develop per the PR template, but develop and main have no common ancestor (gh api repos/kryptobaseddev/cleo/compare/develop...main returns "No common ancestor"). develop is from 2026-03-08 and contains only packages/ct-agents and packages/ct-skills -- the Brain package extraction (commit 725fc423, T969) doesn't exist on that branch. Targeting main as a hotfix per the template's exception. Happy to retarget if there's a different active branch I should use.

Process compliance

• I did not push directly to a protected branch
• This PR comes from a fix/... branch
• Commit messages use <type>(<scope>): <subject> (no T-id since this is an external bug; scope is the package)
• No tag/release work in this PR

Summary

• Fix getCleoHome() on Windows in both @cleocode/brain and @cleocode/studio to append the Data subdir, matching the env-paths convention the CLI uses.
• Correct docs/specs/DATABASE-ARCHITECTURE.md Windows path to match.
• One bug, three files, two commits.

Change type

• Bug fix (non-breaking change that fixes an issue)
• Documentation update

Related issues

Closes #102

Repro (before this PR)

Verified on this Windows host (cleo@2026.4.158, @cleocode/brain@2026.4.161, Node v24.13.0, Win 11):

cleo admin paths --json
# data.cleoHome = C:\Users\<user>\AppData\Local\cleo\Data    (correct: env-paths convention)

node --input-type=module -e "import('@cleocode/brain').then(m => console.log(m.getCleoHome()))"
# C:\Users\<user>\AppData\Local\cleo                          (wrong: missing 'Data')

ls "C:\Users\<user>\AppData\Local\cleo\nexus.db"             # NOT FOUND
ls "C:\Users\<user>\AppData\Local\cleo\Data\nexus.db"        # found, 256 KB

Result: getNexusSubstrate() / getSignaldockSubstrate() silently return 0 nodes despite populated DBs.

After this PR

node --input-type=module -e "import('@cleocode/brain').then(m => console.log(m.getCleoHome()))"
# C:\Users\<user>\AppData\Local\cleo\Data                    (matches CLI)

How was this tested

• Ran pnpm test (Vitest) -- not run; this is a Windows-host-only path resolution change with no existing tests for cleo-home.ts (no __tests__/cleo-home.test.ts in the brain package). Happy to add a test if you want one written.
• Ran pnpm typecheck -- not run locally
• Ran pnpm build -- not run locally
• Tested manually on Windows. Verified that with the patched dist/src/cleo-home.js applied to a global install, getCleoHome() returns %LOCALAPPDATA%\cleo\Data and Brain's nexus/signaldock paths now resolve to existing files (exists: true). Project-tier substrates (tasks/brain/conduit) continue to work unchanged.

CLEO-specific checklist

• Atomic operations: N/A (no writes)
• Validation: N/A (no schema-bearing code)
• Error handling: N/A (pure path resolution)
• No time estimates: confirmed
• Commit messages: fix(brain): ... and docs(database-architecture): ... per CONTRIBUTING.md (T-id omitted because non-release; release-lint hook exits 0 for non-release commits per scripts/hooks/commit-msg-release-lint.mjs)
• Verb standards: N/A (no new commands)

Environment

CLEO version: 2026.4.158 (CLI), 2026.4.161 (@cleocode/brain)
Node version: v24.13.0
OS: Windows 11 Pro 10.0.26200

AI agent disclosure

• This PR was written entirely by a human
• This PR was written with AI agent assistance (human reviewed)
• This PR was written primarily by an AI agent (human supervised)

Notes

Both commits include Signed-off-by: Jordan Calabrese <calabresejordan@gmail.com>.

packages/brain/src/cleo-home.ts notes in its header that it is "a trimmed mirror of packages/studio/src/lib/server/cleo-home.ts ... Kept in sync manually" -- both files are patched together so they stay in sync. Suggest a follow-up to either factor getCleoHome into a shared utility (perhaps in packages/contracts) or replace both with a direct dependency on env-paths, but that's out of scope here.