[BUG] A per-dependency targets: list disables per-file hook target routing

[srobroek]

A per-dependency targets: list disables per-file hook target routing

Problem

Setting a per-dependency targets: list in a consumer apm.yml disables
per-file hook routing for that dependency. A package that ships divergent
per-target hook files (a Claude file and a Codex file that are not
interchangeable) then has every file merged into every active target,
cross-contaminating each tool's config and duplicating shared entries.

targets: was introduced to narrow which targets a dependency installs to; it
should refine routing, not switch it off.

Reproduction

A package ships pkg-claude-hooks.json (a PreToolUse/Skill matcher) and
pkg-codex-hooks.json (a PostToolUse/apply_patch matcher), each also
carrying a shared Bash hook. Consumer:

dependencies:
  - git: owner/pkg
    targets: [claude, codex]

Matchers written to each tool's merged config:

Consumer targets:	.claude/settings.json	.codex/hooks.json	Correct?
(omitted)	PreToolUse:[Skill], Bash:[*]	PostToolUse:[apply_patch], Bash:[*]	yes
[claude, codex]	PreToolUse:[Skill], Bash:[*], PostToolUse:[apply_patch]	PreToolUse:[Skill], Bash:[*], PostToolUse:[apply_patch]	no
[codex]	(not installed)	PreToolUse:[Skill], Bash:[*], PostToolUse:[apply_patch]	no

Even a single-target [codex] contaminates: Codex absorbs the Claude file's
Skill hook. Expected: each file lands only in its intended tool; targets:
only restricts which tools are active.

Reproduced on main (microsoft/apm@49bfdc67) and released 0.24.x/0.25.x.

Root cause

Any per-dependency targets: list sets dep_targets_active = True in
filter_targets_for_dependency (src/apm_cli/install/target_filter.py). That
boolean gates per-file routing at three sites:

• src/apm_cli/integration/hook_integrator.py:1154 (Copilot)
• src/apm_cli/integration/hook_integrator.py:1370 (merged targets: Claude,
  Cursor, Codex, Gemini, Windsurf, Antigravity)
• src/apm_cli/integration/kiro_hook_integrator.py:239 (Kiro)

if not dep_targets_active:
    hook_files = _filter_hook_files_for_target(hook_files, target_key, ...)

When the boolean is true the filter is skipped, so every hook file is handed to
the merge step for every active target, and the merge step does not re-route by
target.

Fix

Proposed in #2259. Remove the dep_targets_active gate at all three sites so
per-file routing always runs. targets: still narrows which targets are active upstream; routing
then places each file only in its intended tool. Universal files and combined
claude-codex manifests are unaffected, and the dep_targets_active chokepoint
assertion in integrate_hooks_for_target still consumes the parameter.

Harness-agnostic (every merge-based target: copilot/vscode, cursor, claude,
codex, gemini, antigravity, windsurf, kiro). A separate issue tracks the design
gap that filename routing was deprecated without a replacement for divergent
per-target files.