Reasoning modes

aiscope ships two reasoning modes. They control which subsystem pairs are even considered for clash detection.

Uniform (default)

Every cross-source pair is a candidate. Maximum recall.

aiscope .
aiscope --diag .

Use Uniform when:

You want to catch everything that might confuse the model.
You have a small, simple repo with one tool and few files.
You're doing the first audit of a new repo.

Specific (`--specific`)

Subsystem-aware filtering via this matrix:

Left subsystem	Right subsystem	Can clash?
`Instructions`	`Instructions`	✅ yes
`Instructions`	`Prompts`	❌ no
`Instructions`	`Agents`	❌ no
`Instructions`	`ChatModes`	❌ no
`Instructions`	`Skills`	❌ no
`Prompts`	`Prompts`	✅ yes
`Agents`	`Agents`	✅ yes
`ChatModes`	`ChatModes`	✅ yes
`Skills`	`Skills`	✅ yes

aiscope --specific .
aiscope check --specific .

Why these rules?

Prompts ↔ Instructions: prompts are intentional one-shot overrides. They should contradict the always-on instructions when the user invokes them.
Agents ↔ everything: agents run with their own context window. What an agent says doesn't reach the main session.
Skills / ChatModes ↔ anything else: these are also opt-in contexts.

Which should I use in CI?

Use --specific in CI:

- run: aiscope check --specific .

It's the right default for most teams — fewer false positives, still catches the conflicts that actually break model behavior.

Use default Uniform locally when you want to see everything.

Note: AgentToolMismatch is unaffected

The --specific flag only filters cross-subsystem clashes. It does not silence AgentToolMismatch diagnostics — those are always reported, because they're always real bugs.

aiscope