editorMode is a documented top-level settings.json key
(code.claude.com/docs/en/settings); ~/.claude.json is documented as
OAuth session / MCP config / per-project trust state / caches, not a
settings store. The current claude_code.preferences ->
modify_dot_claude.json.tmpl injection (PR #718) targets the wrong
file, same category of bug as the tools/files no-op keys already
removed from this same settings block.

Confirmed settings.json is the real, effective location before
adding this: the live ~/.claude/settings.json already had
editorMode = "vim" (from toggling /config previously, not from any
chezmoi-managed source) -- Claude Code itself reads/writes it there.

Also fixed a stale comment referencing the old
ai.command_policy.families / single-file .chezmoidata/ai/command_policy.toml
shape, superseded by this branch's flat commands dict under
.chezmoidata/ai/command_policy/*.toml.

Not removing the ~/.claude.json injection yet -- that file is
modified on the separate open PR #718 branch; removing
claude_code.preferences here risks a merge-order-dependent break of
that script. Left as an explicit follow-up for after both PRs merge.

…njection

editorMode was the only key claude_code.preferences ever injected into
~/.claude.json via modify_dot_claude.json.tmpl. Now that it lives in
claude_code.settings (-> ~/.claude/settings.json, the documented
location, previous commit), that injection is a pure no-op -- and
~/.claude.json itself is documented as OAuth session / MCP config /
trust state / caches, not a place a dotfiles repo should be
templating content into at all.

Deletes modify_dot_claude.json.tmpl and claude_code.preferences
outright rather than leaving inert infrastructure around. This also
makes moot a separate bug found while investigating: the file had
lost its executable bit (required for chezmoi's legacy external-
script modify_ mechanism) and chezmoi diff was rendering its raw
unexecuted Python source as the literal target content -- would have
replaced the live ~2000-line ~/.claude.json with ~46 lines of garbage
had it ever been applied in that state. Deleting the file removes the
bug's entire surface rather than patching a mechanism with no reason
to exist anymore.

Updates dot_claude/AGENTS.md (single managed file now, not two) and
the stale modify_dot_claude.json.tmpl cross-reference in
dot_claude/modify_settings.json.

Supersedes PR #718, which was fixing formatting on the now-deleted
file -- closing that PR instead of merging it.

Ported from PR #718 (being closed, superseded -- the file it fixed,
modify_dot_claude.json.tmpl, was deleted outright in the previous
commit rather than patched). Documents the two sharp edges found
empirically (no .tmpl suffix, no executable bit -- both break
chezmoi's dispatch silently) and the trimSuffix "\n" fix for
toPrettyJson's baked-in trailing newline, plus the general key-
ordering caveat for files another live process also writes to.

…717)

* refactor(ai): flatten command_policy to a command->bool dict

Families + prefixes + add/remove/enabled all existed to work around
chezmoi replacing list values wholesale on collision. Storing entries
as dict keys instead removes the problem at the root: an overlay adds
a command by adding a key, or removes one by setting it false — plain
dict merge, same pattern .chezmoidata/ai/sandbox.toml already uses.

Renders byte-identical output to the schema this replaces (verified
against the live ~/.claude/settings.json and
~/.gemini/antigravity-cli/settings.json applied in PR #716) — pure
schema simplification, no behavior change.

* feat(ai): allow/ask/deny tri-state for command_policy commands

Replaces the true/false value with a string mode matching both tools'
real permission tiers (Claude Code has permissions.allow/.deny/.ask;
Antigravity's docs state "Deny > Ask > Allow" precedence). "ask" (or
an unset command) renders nowhere in either tool -- absence from
allow/deny is what falls back to a normal per-use prompt.

All current commands stay "allow" -- no behavior change, verified by
re-rendering against the live settings files with zero diff. deny
rendering is wired but unexercised (no command uses it yet); the
Antigravity deny(...) key name is inferred from documented precedence
language, not yet live-tested, flagged as a comment in the template.

* docs(ai): move command_policy detail to src/chezmoi/AGENTS.md

Root AGENTS.md keeps a 1-2 sentence summary + link; full schema/
rendering/overlay detail moves to src/chezmoi/AGENTS.md, next to the
Notable cross-cutting features bullet (matches the existing sandboxr
pattern). Not placed inside .chezmoidata/ai/command_policy/ itself --
tried that first and it breaks every template reading chezmoi data
(chezmoi parses every file under .chezmoidata/ as a data source; a
.md file there errors with "unknown format").

* docs(ai): use markdown links instead of backtick paths for cross-references

* fix(ai): antigravity permissions fully replaced, not union-merged

User preference: chezmoi should own permissions.allow/.deny outright
rather than preserving whatever agy's own "always allow" flow wrote
into the live file -- matches Claude's existing full-replace behavior.

Also fixes a real bug this surfaced: $agPermissions (built to carry
an optional "deny" key) was computed but never wired into the actual
$settings dict, which still built permissions inline with only
"allow" -- deny was dead code for this tool, unverified until now.
Confirmed working with a throwaway test entry (not committed).

* refactor(ai): convert both settings.json modify scripts to pure chezmoi:modify-template

Drops the embedded-Python round-trip entirely for both
dot_claude/modify_settings.json and
dot_gemini/antigravity-cli/modify_settings.json, matching the
existing dot_codex/modify_config.toml precedent (fromJson .chezmoi.stdin
-> template logic -> toPrettyJson). Requires dropping both the .tmpl
suffix and the executable bit -- chezmoi's chezmoi:modify-template
dispatch doesn't recognize the file otherwise (confirmed empirically;
the executable-script code path silently takes over instead and
.chezmoi.stdin never gets populated).

toPrettyJson's return value always carries a trailing "\n" that trim
markers can't remove (they only affect surrounding template text, not
a pipeline's runtime value) -- piped through trimSuffix "\n" to match
the no-trailing-newline convention both live files already use.

No behavior change: both verified via chezmoi diff against the live
settings files (zero diff), including the deny bucket (tested with a
throwaway, uncommitted data file, both tools).

* fix(claude): move editorMode to the documented settings.json location

editorMode is a documented top-level settings.json key
(code.claude.com/docs/en/settings); ~/.claude.json is documented as
OAuth session / MCP config / per-project trust state / caches, not a
settings store. The current claude_code.preferences ->
modify_dot_claude.json.tmpl injection (PR #718) targets the wrong
file, same category of bug as the tools/files no-op keys already
removed from this same settings block.

Confirmed settings.json is the real, effective location before
adding this: the live ~/.claude/settings.json already had
editorMode = "vim" (from toggling /config previously, not from any
chezmoi-managed source) -- Claude Code itself reads/writes it there.

Also fixed a stale comment referencing the old
ai.command_policy.families / single-file .chezmoidata/ai/command_policy.toml
shape, superseded by this branch's flat commands dict under
.chezmoidata/ai/command_policy/*.toml.

Not removing the ~/.claude.json injection yet -- that file is
modified on the separate open PR #718 branch; removing
claude_code.preferences here risks a merge-order-dependent break of
that script. Left as an explicit follow-up for after both PRs merge.

* fix(claude): stop managing ~/.claude.json entirely, delete the dead injection

editorMode was the only key claude_code.preferences ever injected into
~/.claude.json via modify_dot_claude.json.tmpl. Now that it lives in
claude_code.settings (-> ~/.claude/settings.json, the documented
location, previous commit), that injection is a pure no-op -- and
~/.claude.json itself is documented as OAuth session / MCP config /
trust state / caches, not a place a dotfiles repo should be
templating content into at all.

Deletes modify_dot_claude.json.tmpl and claude_code.preferences
outright rather than leaving inert infrastructure around. This also
makes moot a separate bug found while investigating: the file had
lost its executable bit (required for chezmoi's legacy external-
script modify_ mechanism) and chezmoi diff was rendering its raw
unexecuted Python source as the literal target content -- would have
replaced the live ~2000-line ~/.claude.json with ~46 lines of garbage
had it ever been applied in that state. Deleting the file removes the
bug's entire surface rather than patching a mechanism with no reason
to exist anymore.

Updates dot_claude/AGENTS.md (single managed file now, not two) and
the stale modify_dot_claude.json.tmpl cross-reference in
dot_claude/modify_settings.json.

Supersedes PR #718, which was fixing formatting on the now-deleted
file -- closing that PR instead of merging it.

* docs: default modify_ scripts to chezmoi:modify-template

Ported from PR #718 (being closed, superseded -- the file it fixed,
modify_dot_claude.json.tmpl, was deleted outright in the previous
commit rather than patched). Documents the two sharp edges found
empirically (no .tmpl suffix, no executable bit -- both break
chezmoi's dispatch silently) and the trimSuffix "\n" fix for
toPrettyJson's baked-in trailing newline, plus the general key-
ordering caveat for files another live process also writes to.

* docs: reformat AGENTS.md prose to one sentence per line