fix: complete planningDir migration for config CRUD, template fill, and verify

[NedMalki-Chief]

Closes #1987

Summary

PR #1484 added planningDir(cwd) and the GSD_PROJECT env var so a workspace can host multiple projects under .planning/{project}/. loadConfig() in core.cjs:256 was migrated at the time, but several CRUD entry points and template/verify helpers were left resolving against planningRoot(cwd). This PR completes that migration.

Full reproduction and affected-sites list in #1987.

The split-brain bug

In any multi-project workspace with GSD_PROJECT set:

• cmdConfigGet, setConfigValue, ensureConfigFile, cmdConfigNewProject all read from and write to .planning/config.json (unrouted)
• loadConfig reads from .planning/{GSD_PROJECT}/config.json (project-routed)

The reader and writer pointed at different files. gsd-tools config-get workflow.discuss_mode returned "unset" in multi-project workspaces even when the value was correctly stored in the project-routed file.

planningPaths() in core.cjs carried a comment that "Shared paths (project, config) always resolve to the root .planning/" which described the original intent, but loadConfig() already contradicted that intent for config.json. This PR resolves the contradiction in favor of loadConfig's behavior so the contract matches the only function that successfully read config.json in the multi-project case.

Commits

1. fix(config): route CRUD through planningDir to honor GSD_PROJECT — fixes the four config.cjs CRUD entry points (cmdConfigNewProject, ensureConfigFile, setConfigValue, cmdConfigGet) and the planningPaths() helper in core.cjs (project + config keys). +15/-11 across 2 files.

2. fix(template): emit project-aware references in template fill plan — cmdTemplateFill plan branch hardcoded @.planning/PROJECT.md, @.planning/ROADMAP.md, @.planning/STATE.md references in the body of generated PLAN.md files. These resolve to nothing in multi-project layouts because the actual files live under .planning/{GSD_PROJECT}/. Routes through planningDir(cwd) and normalizes via the existing toPosixPath helper. +8/-4 in 1 file.

3. fix(verify): planningDir for cmdValidateHealth and regenerateState — cmdValidateHealth resolved projectPath and configPath via planningRoot(cwd) while ROADMAP/STATE/phases/requirements went through planningDir(cwd). The inconsistency reported "missing PROJECT.md" and "missing config.json" in multi-project layouts. The regenerateState repair path (/gsd:health --repair) hardcoded See: .planning/PROJECT.md in the regenerated body, which immediately fails the same reference check it just regenerated for. Both fixed; the unused planningRoot import in verify.cjs was also dropped. +7/-5 in 1 file.

Total: +30/-20 across 4 files.

Backward compatibility

Single-project users (no GSD_PROJECT set) are unaffected. planningDir() falls back to .planning/ when no project is configured, so it returns the same path as planningRoot() in that mode. All existing single-project workflows produce identical output before and after.

The TOCTOU/locking wrappers added in #1944 (withPlanningLock, atomicWriteFileSync) are preserved unchanged — only the path resolution inside them is migrated.

Verification

In a workspace with .planning/projectA/config.json and GSD_PROJECT=projectA:

# Before this PR:
GSD_PROJECT=projectA gsd-tools config-get workflow.discuss_mode
# Error: Key not found

# After this PR:
GSD_PROJECT=projectA gsd-tools config-get workflow.discuss_mode
# "discuss"

Single-project regression check (no GSD_PROJECT set, value stored in .planning/config.json):

gsd-tools config-get workflow.discuss_mode
# Returns the value from .planning/config.json (unchanged behavior)

For the template and verify commits:

# Generated PLAN.md should reference @.planning/{GSD_PROJECT}/PROJECT.md when GSD_PROJECT is set
GSD_PROJECT=projectA gsd-tools template fill plan --phase 01 --plan 99
cat .planning/projectA/phases/01-*/01-99-PLAN.md | grep '@.planning'

# /gsd:health --repair should regenerate STATE.md with a project-aware See: ref
GSD_PROJECT=projectA gsd-tools verify health --repair
cat .planning/projectA/STATE.md | grep 'Project Reference' -A 2

Test plan

• CI passes on the PR branch
• Manual verification: multi-project layout reads config correctly after the fix
• Manual verification: single-project layout unchanged
• gsd-tools verify references no longer reports .planning/PROJECT.md, .planning/ROADMAP.md, and .planning/STATE.md as missing on PLAN.md files generated by template fill in multi-project workspaces

🤖 Generated with Claude Code

[trek-e]

Review: APPROVE

Summary

The split-brain diagnosis is correct: loadConfig() already read through planningDir() (line 256) while all CRUD writers used planningRoot(). This PR resolves the contradiction in favor of loadConfig()'s behavior, which is correct.

Changes verified

config.cjs: Four functions switched from planningRoot → planningDir: cmdConfigNewProject, ensureConfigFile, setConfigValue, cmdConfigGet. All are config CRUD entry points — the change is consistent and complete.

core.cjs (planningPaths): project and config paths now route through planningDir instead of the unrouted root. The comment update explaining the contract change is clear.

template.cjs (cmdTemplateFill): The @.planning/ references in generated PLAN.md body now route through planningDir + toPosixPath — fixes reference resolution in multi-project layouts.

verify.cjs (cmdValidateHealth, regenerateState): projectPath and configPath now use planningDir; the hardcoded See: .planning/PROJECT.md in regenerated STATE.md body now uses the routed path. The unused planningRoot import is dropped.

Backward compatibility

Single-project users unaffected: planningDir() falls back to .planning/ when no GSD_PROJECT is set. The TOCTOU/locking wrappers from #1944 are preserved.

No issues found