fix: preserve install markers for Codex plugin roots

[dongyeop-cmyk]

Summary

• resolve install markers against nested plugin/ roots so marketplace installs and Codex-installed plugin roots share the same marker path
• write the install marker into the durable marketplace plugin root after successful install and repair flows
• cover the marketplace-root marker behavior with setup-runtime and install wiring regressions

Verification

• bun test tests/setup-runtime.test.ts tests/install-non-tty.test.ts tests/plugin-version-check.test.ts

[greptile-apps]

Greptile Summary

This PR preserves install markers for marketplace installs that use a nested plugin/ root. The main changes are:

• Resolve install marker reads, writes, and freshness checks through plugin/.install-version when a marketplace root is passed.
• Write marketplace plugin markers after successful install and repair flows.
• Avoid creating SQLite platform_source indexes before the column exists on legacy databases.
• Add tests for marketplace marker behavior and the legacy SQLite migration path.

Confidence Score: 4/5

This PR needs a small compile fix before merging.

A single contained build-breaking scope error remains in the install command marker write. The marker-path and SQLite migration changes are narrow and covered by tests.

src/npx-cli/commands/install.ts

T-Rex Logs

What T-Rex did

• Reproduced the cacheDir scope issue by running the project typecheck route and performing a narrow TypeScript compile of install.ts; the typecheck stopped before source checking due to missing Bun/Node typings, and the compile reported Cannot find name 'cacheDir' at install.ts(1642,26).
• Verified version-state transitions across two runs; the before/after snapshots show the version values shifting as described, and both runs exited with code 0.
• Compared repair-marketplace marker state before and after execution; the before snapshot showed a cache marker existed with no durable marker, and the after snapshot showed the durable marker existed with a JSON version/bun/uv/installedAt, with the run exiting code 0.
• Compared platform schema states before and after initialization; the before run had an SQLiteError about a missing platform_source column, while the after run shows platform_source exists with default 'claude' and related index tables present, and the constructor reported OK with exit code 0.

_{Ran code and verified through T-Rex}

Important Files Changed

Filename	Overview
src/npx-cli/commands/install.ts	Moves install marker writing after task completion and mirrors marketplace markers, but references cacheDir outside its declaration scope.
src/npx-cli/install/setup-runtime.ts	Resolves install markers and node_modules checks through nested marketplace plugin/ roots when present.
src/services/sqlite/SessionStore.ts	Defers platform-source index creation until the column exists so legacy schema initialization can proceed through later migrations.
tests/install-non-tty.test.ts	Adds source-level tests for marketplace marker writes in install and repair flows.
tests/setup-runtime.test.ts	Adds marker read/write coverage for marketplace roots containing nested plugin/package.json.
tests/sqlite/session-store-migrations.test.ts	Adds a legacy pre-platform_source migration fixture verifying initialization no longer crashes and preserves data.

Sequence Diagram

%%{init: {'theme': 'neutral'}}%%
sequenceDiagram
  participant Installer as runInstallCommandInner
  participant Runtime as setup-runtime
  participant Cache as Versioned cache root
  participant Market as Marketplace root
  Installer->>Runtime: ensureBun / ensureUv
  Installer->>Cache: installPluginDependencies(cacheDir)
  Installer->>Runtime: writeInstallMarker(cacheDir, versions)
  Runtime->>Cache: .install-version
  alt marketplace plugin/package.json exists
    Installer->>Runtime: writeInstallMarker(marketplaceDirectory(), versions)
    Runtime->>Market: resolve to plugin/.install-version
  end

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sequenceDiagram
  participant Installer as runInstallCommandInner
  participant Runtime as setup-runtime
  participant Cache as Versioned cache root
  participant Market as Marketplace root
  Installer->>Runtime: ensureBun / ensureUv
  Installer->>Cache: installPluginDependencies(cacheDir)
  Installer->>Runtime: writeInstallMarker(cacheDir, versions)
  Runtime->>Cache: .install-version
  alt marketplace plugin/package.json exists
    Installer->>Runtime: writeInstallMarker(marketplaceDirectory(), versions)
    Runtime->>Market: resolve to plugin/.install-version
  end

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_{Reviews (2): Last reviewed commit: "fix: tolerate pre-platform-source sessio..." | Re-trigger Greptile}

[greptile-apps]

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[greptile-apps]

Restore cacheDir scope
cacheDir is declared inside the runtime setup task at line 1597, so this post-runTasks marker write is outside its block scope and the TypeScript build fails with Cannot find name 'cacheDir'. Hoist const cacheDir = pluginCacheDirectory(version) before the tasks are created, or recompute it here before calling writeInstallMarker.

Artifacts

Repro: project typecheck attempt output showing missing type definitions before source checking

• Keeps the command output available without making the summary code-heavy.

Repro: narrow TypeScript compile output showing Cannot find name cacheDir at install.ts line 1642

• Keeps the command output available without making the summary code-heavy.

_{Ran code and verified through T-Rex}