Runtime tools hardcode ~/.claude, ignoring the config root the installer honors (56 of 161 TOOLS files)

[sabo961]

Summary

DeployCore.ts correctly honors a non-default config root (CLAUDE_CONFIG_DIR), but 56 of the 161 tools in LIFEOS/TOOLS/ resolve their paths from homedir() + ".claude" instead of the detected config root. The install succeeds; the installed system then reads and writes outside its own tree.

INSTALL.md §2 states the intent explicitly — "Every path below comes from this — don't assume ~/.claude or any single harness." The installer follows that rule. The runtime does not.

Reproduction

Verified on macOS 26.4.1, arm64, bun 1.3.14, LifeOS 7.40.4 (ce046f2):

export CLAUDE_CONFIG_DIR="$HOME/.lifeos"
cd <release>/LifeOS
bun Tools/DetectEnv.ts        # configRoot: /Users/sabo/.lifeos  ✓ correct
bun Tools/ScanConflicts.ts    # clean, no collisions
bun Tools/DeployCore.ts --apply

DeployCore deploys correctly into ~/.lifeos (57 skills, full runtime), then fails on a post-install step:

GenerateKnowledgeSchemaDoc exited 1:
ENOENT: no such file or directory,
open '/Users/sabo/.claude/LIFEOS/MEMORY/KNOWLEDGE/_schema.md'

The tool was launched from /Users/sabo/.lifeos/LIFEOS/TOOLS/ and wrote to /Users/sabo/.claude/.

Source — LIFEOS/TOOLS/GenerateKnowledgeSchemaDoc.ts:24:

const OUT = pathResolve(homedir(), ".claude/LIFEOS/MEMORY/KNOWLEDGE/_schema.md");

Scope

Measured with grep over *.ts in ~/.lifeos/LIFEOS/TOOLS/ only. Hooks, skills, and the PULSE tree were not scanned — the real number is likely higher, not lower.

	count
.ts files in LIFEOS/TOOLS/	161
hardcode homedir() + .claude (5 syntactic variants)	56
mention .claude anywhere (incl. strings, help text)	131
read CLAUDE_CONFIG_DIR	3

Of the hardcoding files, only 7 offer an env escape hatch (LIFEOS_DIR, CORTEX_MEMORY_ROOT), and nothing in the install sets those. Setting an env var is therefore not a workaround — it would cover 7 of 56.

Representative examples:

AgentWatchdog.ts:38   process.env.LIFEOS_DIR || join(homedir(), ".claude", "LIFEOS")
ActivityParser.ts:25  path.join(homedir(), ".claude")
CarrierProbe.ts:38    join(homedir(), ".claude")
Cortex.ts:283         ... ?? join(homedir(), ".claude/LIFEOS/MEMORY")
DoctrineReplay.ts:26  join(homedir(), ".claude/LIFEOS/MEMORY/WORK")
HealthSnapshot.ts:34  join(homedir(), ".claude/LIFEOS/USER/HEALTH/snapshots")

Why this matters beyond a failed post-install step

The visible symptom is one tool exiting 1. The invisible one is worse: on a machine where ~/.claude exists but belongs to something else, the failure is silent.

That is our case. This machine runs two separate Claude config trees — ~/.claude and a second one under a different config root. With LifeOS installed into the second tree, Cortex memory, WORK directories, health snapshots, and the knowledge schema would all resolve into the first tree. Nothing errors; the data simply lands in the wrong house and the two installations quietly interleave.

GenerateKnowledgeSchemaDoc failed loudly here only because ~/.claude/LIFEOS/ did not exist. Had it existed, the install would have reported success while writing into a directory it does not own.

Suggested fix

A single shared resolver used by every tool, seeded from the same detection the installer already performs — e.g. LIFEOS/TOOLS/lib/configRoot.ts exporting a configRoot() that reads CLAUDE_CONFIG_DIR (or a LIFEOS_DIR written at install time) and falls back to ~/.claude only when neither is set. The three tools that already read CLAUDE_CONFIG_DIR show the intended shape.

A deterministic gate would prevent regression, in the spirit of the 7.40.4 release notes ("every finding must also become a deterministic catch"): fail the cut if any file under LIFEOS/ contains homedir() joined to a literal .claude. That check is one grep and would have caught all 56.

Environment

• macOS 26.4.1 (arm64), bun 1.3.14, git 2.50.1
• LifeOS 7.40.4, commit ce046f2
• Harness: Claude Code, configRoot detected correctly as the non-default path
• Install path: additive, into an empty directory, no pre-existing LifeOS

---

Filed after a parallel install performed specifically to test upgrade safety from a pre-7.x tree in a non-default config root. Happy to test a patch against the same setup.

[danielmiessler]

Landed, as one sweep: the resolver now lives in LIFEOS/TOOLS/Paths.ts (CLAUDE_CONFIG_DIR, then LIFEOS_SKILLS_DIR, then ~/.claude), 169 tool and hook files were rewritten to call it, and /ic now fails on any new config-root literal outside the resolver and the five deny/allow guards that keep the home path on purpose. Proven with a scratch root: Doctor, StateEvidence and the usage aggregator write only under it, and with no env set they still write to ~/.claude. Doing the sweep here rather than merging the PR versions kept months of local change intact. Next release. Thanks.