Agent Note: Regroup packages/ by measured clustering

Status: implemented

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Problem

The two-level packages/<group>/<pkg> hierarchy (original decision) had drifted since June: 167 packages sat in 42 groups, and several group boundaries no longer matched how the packages actually cluster.

ui/ mixed four unrelated planes: the human terminal channel (tui), the SDK's JSON-RPC server half (jsonrpc, whose peer dependency on dsh-sdk-protocol binds it to the SDK wire stack), the human-interaction seams (user-questions, user-approval, permission, tool-ask-user, commands), and channel-neutral boot glue (app-boot). Its own README narrated the mixture instead of stating a role.
The session family was fragmented across five groups — session-persistence/, session-projection/, session-query/, session-title/, and telemetry/ — although the measured dependency edges tie them together (query → persistence, title → projection, projection → persistence; see docs/module-graph.md).
The timeout/ group for a tool-call guard collided with util/timeout, the generic promise utility.
cordis/ named its group after the framework every package is built on, so the name discriminated nothing; its single package tool-cordis is the runtime self-modification toolset.

The north star for the regrouping: closely clustered packages share a group. A cluster is measured — peer-dependency edges and co-change — not thematic. An isolated seam family may stand alone as a small group; the failure mode to avoid is the grab-bag whose name describes no single role.

Decision

Five regrouping decisions remain current; every other group keeps its prior boundary and contents (the dependency analysis confirmed the capability families — shell/, terminal/, code-runtime/, sandbox/, subprocess/, fs/, lsp/, web/, skill/, and the rest — were already drawn correctly). The original sixth decision collected the SDK project initializer, launcher tooling, and runtime JSON-RPC packages under scaffold/; removing that unreleased toolchain deleted the project tooling and moved the surviving runtime trio to sdk/. The later repository naming contract owns the shell/, terminal/, and extensions/ group names and the two package names that this decision deferred.

Group	Members (folder names)	From
`session/`	session-persistence, session-persistence-jsonl, session-persistence-sqlite, session-checkpoint-policy, session-projection, session-projection-cache, session-title, session-title-llm, session-title-first-prompt-llm, session-title-all-prompts-llm, session-telemetry, session-telemetry-otel	`session-persistence/` + `session-projection/` + `session-title/` + `telemetry/`
`interaction/`	user-questions, user-approval, permission-presets, tool-ask-user, commands, tui	`ui/`
`boot/`	app-boot	`ui/`
`guard/`	repeat-tool-reminder, timeout-policy	`guard/` + `timeout/`
`extensions/`	tool-cordis	`cordis/`

session/ is the durable session data plane: the persistence seam with its backends and checkpoint policy, the projection fold that serves whole values from that log, log-backed titles, and OTel reporting. The title fold is itself load-bearing for the read side (session-query peer-depends on dsh-session-title), so titles belong with the data plane, not in a derived-services annex. The plain name is deliberate (prefer names a human would say); the nearby core/session package remains the live in-memory service, while this group is the durable family around it. session-query/ stays a standalone group — the read/tool surface has its own model tools and SQLite FTS backend and is consumed independently of persistence internals.
interaction/ is the human-collaboration plane plus the terminal channel that answers it: the question/approval seams, the permission preset, the model-facing ask_user_question tool, the human-command registry (plan-mode and command-goal already consume commands together with the interaction seams), and tui — the interactive channel is the plane's richest provider and consumer (peer edges to commands and user-questions), and a one-package tui/ group would spend a top-level name on one plugin.
boot/ is a role-complete single-package group: the shared bin boot glue that belongs to no channel and no assembly (consumed by apps/cli and the examples/ demo bins).
guard/ keeps its documented role, loop-hygiene guards, and gains the tool-call timeout enforcer, dissolving the one-package timeout/ group whose name collided with util/timeout.
extensions/ names the role cordis/ obscured: the toolset with which the agent inspects and mounts plugins in its own live runtime, and the landing zone for future self-modification packages.

42 groups became 39; the win is clustering correctness and truthful names, not count.

Later naming decisions

The repository naming contract resolves the two names that this move deliberately deferred. @deepseek-ai/dsh-sdk-jsonrpc-server names the JSON-RPC server half of the runtime SDK protocol. @deepseek-ai/dsh-tool-call-timeout-policy names the exact operation limited by the policy while keeping its guard/timeout-policy/ home. Their release-blocking FIXME markers are removed with those renames.

What the move touched

The moves landed as pure git mv moves, so rename detection carries the history. A group move touched: the moved package's tsconfig.json relative references and every dependent's entry (including the apps/cli project references), the tsconfig aggregate and path maps, group READMEs, the packages/README.md hierarchy table, the root AGENTS.md layout map, regenerated artifacts (docs/module-graph.md, path-embedding catalogs, and the lockfile's importer keys), and root-relative packages/... citations in prose and gate scripts. Remaining group-path referents (workspace configs, test globs, lint keys) were found mechanically by the acceptance gates failing loud — the repository's own misconfiguration rule.

A group move did not touch: npm names, imports, cordis.yml configs, snapshot fixtures, the pnpm-workspace.yaml/tsdown globs (both packages/*/*), or the Python runtime manifest — all reference packages by npm name.

client/ and host/ were out of scope and are unchanged.

Alternatives considered

Coarse domain buckets (exec/ = subprocess+sandbox+bash+pty+code-runtime, workspace/ = fs+lsp+workspace, orchestration/ = subagent+workflow+tasks, knowledge/ = web+skill, collab/ = plan+todo+goal; ~16 groups). Rejected: the measured graph contradicts the merges. sandbox and subprocess are shared infrastructure consumed across families (bash ×5, fs ×5, pty, lsp, mcp, and subagent edges), web ↔ skill have zero edges, and a large bucket reproduces the ui/ grab-bag at a larger scale.

Abstract layer names (capability/, policy/, extension/, provider/). Rejected: they describe every plugin equally badly, and a capability/ bucket would hold ~50 packages.

A full npm rename sweep (dsh-<group>-<pkg> for every package). Rejected: npm names are flat, so group-prefixing adds churn across imports, configs, and fixtures with no disambiguation gain; targeted FIXME-tracked renames cover the actual collisions.

Performing the deferred renames inside the reorganization. Rejected: renames multiply open-PR conflicts and destroy the pure-move review property. The remaining FIXME markers keep them visible release blockers to resolve as small follow-up PRs.

A two-way session split (session-core/ + session-utils/). Rejected: query belongs to neither side cleanly, and session-core invites confusion with core/session (dsh-session, the live in-memory service, which stays in core/).

A three-way session split (session-store/ + session-query/ + session-utils/). Rejected: session-utils/ was a negatively-defined annex ("derived, nothing load-bearing depends on it") — the grab-bag shape the north star forbids, and factually wrong besides (session-query peer-depends on dsh-session-title). The invented compound names also read machine-generated; one plain session/ group says what a human would say. Query stays standalone regardless: it is an independently consumed read surface with its own tool package and backend.

Recomposing ui/ as a single channels/ group (tui + jsonrpc + acp + interaction seams + boot). Rejected: the same grab-bag under a new name — those packages serve four planes, jsonrpc's measured cluster is the SDK wire stack, and acp/ is an automation transport, not a human channel.

A standalone one-package tui/ group. Rejected: tui is the interaction plane's primary provider/consumer (peer edges to commands, user-questions), and a top-level name spent on one plugin adds a group without adding information; it folds into interaction/.

Moving app-boot to apps/. Rejected: apps/ is the assembly tier over the package tier, and dsh-app-boot is a package-tier library — placing it in apps/ would invert the tiers and put a workspace library outside the packages/*/* build globs. It stays a package; boot/ is its role-complete home.

Moving tool-cordis into core/. Rejected: self-modification is its own product seam, expected to grow; the spine stays minimal. The group was first named self-evolve/; the name settled on extensions/ as the plainer term.

Renaming context/ to request-context/. Rejected: within this tree the group is unambiguous in situ; the churn is unjustified.

Consequences

The five still-current regrouped families hold the listed members; the groups ui/, telemetry/, timeout/, cordis/, session-persistence/, session-projection/, and session-title/ no longer exist. The regrouping itself changed no npm names. The later SDK toolchain removal intentionally changed the package set and restored sdk/ as the precise home of the runtime SDK trio. Two FIXME markers pin the remaining deferred renames; a FIXME that later proves wrong must be removed explicitly with rationale, never silently dropped.
What pins the result: pnpm run typecheck, the unit suites of every moved group, verify-package-paths, verify-md-links, and the corpus-wide translation pairing all pass on the moved tree; the group-scoped test globs in vitest.snapshot.config.ts were rewritten with the moves so the suites collect the same test files as before (a fail-open glob would silently drop coverage).
Every open PR touching a moved file rebases across the move once; rename detection resolves most hunks mechanically.
Single-package groups remain (boot/, extensions/, and existing ones such as acp/). Accepted deliberately: each is role-complete rather than a fragment of a family, and a truthful small group beats a nominal merge.
The sdk/ role folders map explicitly to their npm names in tsconfig.base.json; the server/ mapping resolves to @deepseek-ai/dsh-sdk-jsonrpc-server.
What this gave up: nothing functional — the change is navigational. Muscle memory and external links to old GitHub paths break, which is acceptable pre-release with no external consumers.

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