fix(runtime-host): keep the preferred location when registering a project path

[jsiu93]

Summary

Project preference is derived from location usage (newest lastUsedAt among available locations), and registration wrote the registration timestamp into the location it touched. So runtime-host project add <second checkout> also selected that checkout, and every later project-targeted Session started there.

This adds an optional prefer field to the project.register request. Omitted or true keeps today's behavior; false adds or refreshes a location without recording usage (a new location is stored with lastUsedAt: 0, an existing one keeps its timestamp). A new project still establishes its sole location as the initial preference.

The CLI runtime-host project add now sends prefer: false by default and gains --prefer for callers who mean to select the path. Desktop is unchanged: its registration call sites omit the field, so the folder-open flow (register, then create a project-targeted Session in that folder) behaves as before.

Fixes#3572

Review focus

Opened as a draft for a design check before review effort goes in. Two decisions here are yours to make, and I would rather adjust than argue:

1. Shape of the API. This puts an optional prefer on the existing project.register request, so project add stops selecting by default and --prefer opts in. The alternative is to keep registration as it is and add a separate "use this location" operation (a project use <path> verb), which matches how docker context use or kubectl config use-context separate creating from selecting. Both need the same epoch bump; I picked the smaller diff.
2. The compatibility epoch bump (41 to 42) for a CLI default. If you would rather not spend an epoch on this, say so and I will reduce the PR to the issue plus the storage test coverage.

Compatibility epoch

Bumped from 41 to 42. The registration request is a closed shape, so an epoch-41 Host rejects the new field and a new CLI always sends it. Precedent: 8346fbb92 bumped 36 to 37 when an optional text field was added to another exact catalog request.

Verification

New regression tests, all red before the change and green after:

• storage project-catalog.test.ts: a second location registered with prefer: false leaves preferredPath unchanged; re-registering the non-preferred location with prefer: false leaves it unchanged; registration with the option omitted still selects the path; a later touch on the new location makes it preferred; a new project still gets its sole location as preference.
• runtime-host project-catalog-protocol.test.ts and project-catalog-coordinator.test.ts: project.register accepts prefer: false and the returned record keeps preferredPath; a non-boolean prefer is rejected; protocol.test.ts pins epoch 42.
• cli runtime-host-operator-command.test.ts: project add sends prefer: false by default and prefer: true with --prefer.

Suites, on Node 24.19.0 (the version main CI uses):

npm --workspace @maka/storage test# tests 914, pass 900, skipped 14, fail 0
npm --workspace @maka/runtime-host test# tests 1113, pass 1113, fail 0
npm --workspace maka-agent test# tests 401, pass 401, fail 0

Typecheck passed in the three workspaces. biome lint and biome format reported no fixes on the 12 changed files; git diff --check clean.

Live, fresh Host roots, worktree named aaa-worktree so it sorts before repository:

CLI from main: add repository, add aaa-worktree -> preferredPath: aaa-worktree
CLI from this PR: add repository, add aaa-worktree -> preferredPath: repository
CLI from this PR: add aaa-worktree --prefer -> preferredPath: aaa-worktree

Not run: full monorepo npm test, root-wide typecheck/lint/format, Desktop suites, Windows or Linux.

AI use

Select exactly one:

• No generative tool made a substantive contribution
• Generative tooling made a substantive contribution

Tool(s) and scope: pi (gpt-5.6-sol) traced the storage, protocol, Desktop and Session-creation paths, wrote the implementation and the regression tests, ran the live and compatibility checks, and drafted this description. Claude Code chose the design, reviewed the diff, re-ran the three suites, and edited this text. The commit carries the trailer.

Generated-by: pi (gpt-5.6-sol)

Checklist

• Tests cover the change and fail without it
• Lint, format, typecheck and the affected suites pass locally

Does this PR entail a change in behavior?

• Yes — described under Summary above
• No

[Astro-Han]

Reviewed exact head f896059. Coverage: storage registration preference semantics across existing/new linked-worktree locations and later touch; Runtime Host protocol/coordinator defaulting and strict boolean decoding; CLI default and explicit --prefer transport; existing Desktop callers retaining prefer-by-default behavior; catalog ordering, path normalization, and transactional mutation paths. Exclusions: real multi-process CLI/Desktop smoke testing and visual/UI behavior. Local Core→Storage→Runtime Host→CLI builds passed, with 78 focused tests green; hosted exact-head test is green. No P0–P3 findings. The branch currently conflicts with main only in packages/runtime-host/src/protocol/index.ts; resolution should preserve both compatibility additions/comment blocks and advance from current main epoch 43 rather than choosing the PR epoch 42 verbatim.

[Astro-Han]

Incremental re-review at exact head 2b639688040c317eef75b1d96a1e01be07fc3b4c. APPROVE — no P0–P3.

This confirms the earlier approval, which was bound to f896059b. I did not re-review the whole change; I verified that the only difference since that approval is the epoch realignment, and that it is correct.

What changed since f896059b

Comparing each file's patch content against its own merge-base (efddab2f then, 84ed9a31 now), 11 of the 12 touched files have byte-identical patches. The single difference is in packages/runtime-host/src/protocol/index.ts:

• RUNTIME_HOST_COMPATIBILITY_EPOCH moved from 42 to 45
• the ledger comment was re-anchored from "Epoch-41 Hosts" to "Epoch-44 hosts", and the intervening 44 / 43 entries from main were kept

Why 45 is the right value

Current main (04836d3b8) is at 44. 45 is the next value, so the monotonic-progression rule holds and no Host that speaks 44 will silently accept the new optional location field on the closed registration input.

One merge-order caveat for maintainers, not a defect in this PR: #3467, #3316, #3376, #3651 and #2521 are also currently claiming 45. Whichever merges first advances main; the rest will need to re-bump. That is inherent to a single global counter, not something this author did wrong.

Gates at this exact head

• test — terminal success
• mergeable — MERGEABLE / CLEAN
• unresolved review threads — 0
• the check set is the correct triggered set for these paths

中文

在 exact head 2b639688 上做的增量复审，结论 APPROVE，无 P0–P3。原批准绑在 f896059b，本次不重审全量，只核"自那次批准以来变了什么"。

各文件对各自 merge-base 的 patch 逐一比对：12 个文件里 11 个逐字节相同，唯一变化是 protocol/index.ts 的 epoch 42→45 与注释重排。main 现在是 44，45 单调正确。

提醒（非本 PR 缺陷）：#3467、#3316、#3376、#3651、#2521 目前都在争 45，谁先合谁把 main 推上去，其余需要重新递增。这是全局单调计数器本身的性质。

门禁：test 终态绿、CLEAN、零未决线程。

[Astro-Han]

I rebased this branch onto the latest main for you. The new head is 691ab3de4.

The conflict was the protocol epoch: main has already moved RUNTIME_HOST_COMPATIBILITY_EPOCH to 46 (queue.entry.update), while this branch still set it to 45. Merging as-is would have overwritten epoch 46 and broken mixed-version handshakes. In the rebase I renumbered this PR's change to epoch 47, kept the 46 and 45 notes, and merged the three epoch assertions in the protocol test — yours now reads > 46. The functional change itself is untouched.

Local verification: runtime-host and storage typecheck cleanly, and all 78 protocol / project-catalog tests pass. Once CI is green on the new head I will re-review and move this along.

简体中文

我帮这个分支 rebase 到了最新的 main（新 head 691ab3de4）。

冲突点是协议 epoch：main 上已经把 RUNTIME_HOST_COMPATIBILITY_EPOCH 推到了 46（queue.entry.update），而这条分支还停在把它改成 45。直接合并会覆盖掉 46 这一档，混版握手就失效了。rebase 时我把这个 PR 的改动重新编号为 epoch 47，保留了 46/45 的说明，并把 protocol 测试里三条 epoch 断言合到一起，你这条断言相应改成 > 46。功能改动本身没动。

本地验证：runtime-host 与 storage 类型检查通过，protocol / project-catalog 相关 78 项测试全过。等新 head 的 CI 跑绿后我再重新 review 并推进合并。

[Astro-Han]

Approving at 691ab3de4. CI is terminal green on this exact head (run 32708235015), including the Release contracts step that failed on the previous attempt — that one was flaky, not caused by this branch.

Since I rebased this branch myself, I re-checked the result rather than relying on the earlier approvals, which were bound to f896059b and 2b639688 and no longer describe this code.

What I verified:

• Epoch lands correctly.main publishes 46 and this head publishes 47, so the bump is sequential over the current base. One other open PR also carries 47; whichever merges second will need 48, and that is a coordination matter rather than anything wrong here.
• No persisted format change.ProjectRegistrationOptions.prefer is an in-memory option; PersistedProject is untouched. An existing catalog file loads unchanged, so there is no upgrade path to worry about.
• Merged against current main, not just the PR head. The merge is clean, and on the merged tree packages/storage project-catalog tests pass 22/22 and the runtime-host project-catalog coordinator, project-catalog protocol, and bootstrap protocol tests pass 56/56.
• The maka-agent build fails in my local checkout, but byte-identically on a clean main checkout in the same environment (@maka/eval unbuilt, a pi-tui version mismatch). That is stale local workspace state, not attributable to this change; hosted CI covers those tests and is green.

Merging now.

简体中文

在 691ab3de4 上给出 approve。这个 exact head 的 CI 是终态绿（运行记录 32708235015），其中包括上一次失败的 Release contracts 步骤——那次是偶发，不是这个分支造成的。

由于这个分支是我自己 rebase 的，我重新核对了结果，而没有沿用之前的 approve：它们绑在 f896059b 和 2b639688 上，已经不描述当前代码了。

我核对了这些：

• epoch 落点正确。main 发布的是 46，这个 head 发布的是 47，因此这次提升在当前基线上是连续的。另有一个开放 PR 也占用了 47，后合入的那个需要改成 48；这属于协调事项，不是这里有问题。
• 没有持久化格式变更。ProjectRegistrationOptions.prefer 是内存中的选项，PersistedProject 未被改动。既有的 catalog 文件可以原样加载，因此不存在需要考虑的升级路径。
• 是对当前 main 做了合并验证，而不只是看 PR head。 合并干净，并且在合并后的树上，packages/storage 的 project-catalog 测试 22/22 通过，runtime-host 的 project-catalog coordinator、project-catalog protocol 和 bootstrap protocol 测试 56/56 通过。
• maka-agent 在我本地检出上构建失败，但在同一环境下干净 main 检出上的报错逐字节一致（@maka/eval 未构建、pi-tui 版本不匹配）。这是本地 workspace 状态过期，与本次改动无关；这部分测试由托管 CI 覆盖，且是绿的。

现在合并。